Merge pull request #6154 from mvdbeek/fix_bcftools_gtcheck_typo

Fix ection typo in bcftools_gtcheck
galaxyproject · Jul 16, 2024 · bfc4ff4 · bfc4ff4
2 parents d5891ff + ec8da19
commit bfc4ff4
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Showing 8 changed files with 39 additions and 39 deletions.
diff --git a/tools/bcftools/bcftools_call.xml b/tools/bcftools/bcftools_call.xml
@@ -139,14 +139,14 @@ ${section.variants_only}
                         </when>
                         <when value="alleles">
                             <expand macro="macro_restrictions_file" type="target" label_type="Target" />
-                            <param name="insert_missed" argument="--insert-missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert missed" help="Output also sites missed by mpileup but present in -T" />
+                            <param argument="--insert-missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert missed" help="Output also sites missed by mpileup but present in -T" />
                         </when>
                         <when value="trio">
                             <expand macro="macro_restrict" type="target" label_type="Target" />
                             <expand macro="macro_novel_rate" />
                         </when>
                     </conditional>
-                    <param name="prior_freqs" argument="--prior-freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies">
+                    <param argument="--prior-freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies">
                         <help>
 <![CDATA[
 For example: --prior-freqs REF_AN,REF_AC
@@ -172,7 +172,7 @@ For example: --prior-freqs REF_AN,REF_AC
                         </when>
                     </conditional>
                     <expand macro="macro_restrict" type="target" label_type="Target" />
-                    <param name="pval_threshold" argument="--pval-threshold" type="float" value="0.5" optional="true" label="Pval Threshold" help="Accept variant if P(ref|D)&lt;FLOAT" />
+                    <param argument="--pval-threshold" type="float" value="0.5" optional="true" label="Pval Threshold" help="Accept variant if P(ref|D)&lt;FLOAT" />
                 </when>
             </conditional>
         </section>
@@ -184,23 +184,23 @@ For example: --prior-freqs REF_AN,REF_AC
                 <option value="Y">Y - Treat male samples as haploid and female as no-copy, regardless of the chromosome name"</option>
                 <option value="1">1 - Treat all samples as haploid</option>
             </param>
-            <param name="ploidy_file" argument="--ploidy-file" type="data" format="tabular" optional="true" label="Ploidy file" help="Space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
+            <param argument="--ploidy-file" type="data" format="tabular" optional="true" label="Ploidy file" help="Space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
             <expand macro="macro_restrict" />
             <expand macro="macro_samples" />
         </section>
         <section name="sec_input_output" expanded="false" title="Input/output Options">
-            <param name="group_samples" argument="--group-samples" type="boolean" truevalue="--group-samples -" falsevalue="" label="Single Sample Calling" help="Group samples by population for single-sample calling (-G - is the only option implemented so far)" />
-            <param name="keep_alts" argument="--keep-alts" type="boolean" truevalue="--keep-alts" falsevalue="" label="Keep alts" help="Output all alternate alleles present in the alignments even if they do not appear in any of the genotypes" />
-            <param name="format_fields" argument="--format-fields" type="text" value="" optional="true" label="Comma-separated list of FORMAT fields to output for each sample"
+            <param argument="--group-samples" type="boolean" truevalue="--group-samples -" falsevalue="" label="Single Sample Calling" help="Group samples by population for single-sample calling (-G - is the only option implemented so far)" />
+            <param argument="--keep-alts" type="boolean" truevalue="--keep-alts" falsevalue="" label="Keep alts" help="Output all alternate alleles present in the alignments even if they do not appear in any of the genotypes" />
+            <param argument="--format-fields" type="text" value="" optional="true" label="Comma-separated list of FORMAT fields to output for each sample"
                    help="Currently GQ and GP fields are supported" >
                 <validator type="regex" message="FORMAT terms separated by commas">^([A-Za-z]+(,[A-Za-z]+)*)?$</validator>
             </param>
-            <param name="keep_masked_ref" argument="--keep-masked-ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" label="Keep masked reference alleles" help="Output sites where REF allele is N" />
-            <param name="skip_variants" argument="--skip-variants" type="select" optional="true" label="Skip variants" help="Skip indels/SNP sites">
+            <param argument="--keep-masked-ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" label="Keep masked reference alleles" help="Output sites where REF allele is N" />
+            <param argument="--skip-variants" type="select" optional="true" label="Skip variants" help="Skip indels/SNP sites">
                 <option value="indels">indels</option>
                 <option value="snps">snps</option>
             </param>
-            <param name="variants_only" argument="--variants-only" type="boolean" truevalue="--variants-only" falsevalue="" label="Output variant sites only" />
+            <param argument="--variants-only" type="boolean" truevalue="--variants-only" falsevalue="" label="Output variant sites only" />
             <expand macro="macro_output_tags">
                 <option value="INFO/PV4">INFO/PV4: P-values for strand bias, baseQ bias, mapQ bias and tail</option>
                 <option value="FORMAT/GQ">FORMAT/GQ: Phred-scaled genotype quality</option>

diff --git a/tools/bcftools/bcftools_cnv.xml b/tools/bcftools/bcftools_cnv.xml
@@ -181,14 +181,14 @@ bcftools @EXECUTABLE@
                     <param name="lrr_weight" type="hidden" value="0" />
                 </when>
             </conditional>
-            <param argument="--err-prob" name="err_prob" type="float" value="1e-4" label="Err Prob" help="Uniform error probability" />
-            <param argument="--same-prob" name="same_prob" type="float" value="0.5" min="0" max="1" label="Same Prob">
+            <param argument="--err-prob" type="float" value="1e-4" label="Err Prob" help="Uniform error probability" />
+            <param argument="--same-prob" type="float" value="0.5" min="0" max="1" label="Same Prob">
                 <help>
                     The prior probability of the query and the control sample being the same. 
                     Setting to 0 calls both independently, setting to 1 forces the same copy number state in both. (default: 0.5)
                 </help>
             </param>
-            <param argument="--xy-prob" name="xy_prob" type="float" min="0." max="1." label="Xy Prob" value="1e-9">
+            <param argument="--xy-prob" type="float" min="0." max="1." label="Xy Prob" value="1e-9">
                 <help>
                     The HMM probability of transition to another copy number state. 
                     Increasing this value leads to smaller and more frequent calls. 

diff --git a/tools/bcftools/bcftools_consensus.xml b/tools/bcftools/bcftools_consensus.xml
@@ -139,7 +139,7 @@ ${section.iupac_codes}
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <expand macro="test_using_reference" ref="consensus.fa" />
             <param name="input_file" ftype="vcf" value="consensus.vcf" />
             <param name="mask" ftype="tabular" value="consensus.tab" />
@@ -155,7 +155,7 @@ ${section.iupac_codes}
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <expand macro="test_using_reference" select_from="cached" ref="consensus" />
             <param name="input_file" ftype="vcf" dbkey="?" value="consensus.vcf" />
             <param name="mask" ftype="tabular" value="consensus.tab" />
@@ -171,7 +171,7 @@ ${section.iupac_codes}
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <expand macro="test_using_reference" ref="consensus.fa" />
             <param name="input_file" ftype="vcf" value="consensus.vcf" />
             <param name="mask" ftype="tabular" value="consensus.tab" />
@@ -186,7 +186,7 @@ ${section.iupac_codes}
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <expand macro="test_using_reference" ref="consensus.fa" />
             <param name="input_file" ftype="vcf" value="consensus.vcf" />
             <section name="sec_restrict">
@@ -199,7 +199,7 @@ ${section.iupac_codes}
             </output>
         </test>
         <!--Test absent option-->
-        <test>
+        <test expect_num_outputs="1">
             <expand macro="test_using_reference" ref="consensus.fa" />
             <param name="input_file" ftype="vcf" value="consensus.vcf" />
             <section name="sec_restrict">
@@ -216,7 +216,7 @@ ${section.iupac_codes}
             </assert_command>
         </test>
         <!--Test mask options -->
-        <test>
+        <test expect_num_outputs="1">
             <expand macro="test_using_reference" ref="consensus.fa" />
             <param name="input_file" ftype="vcf" value="consensus.vcf" />
             <section name="sec_restrict">

diff --git a/tools/bcftools/bcftools_convert_from_vcf.xml b/tools/bcftools/bcftools_convert_from_vcf.xml
@@ -145,7 +145,7 @@ $convert.sex_info.sex_info_lines.__str__.strip().replace(' ','\t')#slurp
         <data name="output_samples" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.samples"/>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_file" ftype="vcf" value="convert.vcf" />
             <param name="convert_to"  value="gen_sample" />
             <output name="output_gen">
@@ -159,7 +159,7 @@ $convert.sex_info.sex_info_lines.__str__.strip().replace(' ','\t')#slurp
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_file" ftype="vcf" value="convert.vcf" />
             <param name="convert_to"  value="gen_sample" />
             <param name="tag"  value="GP" />
@@ -170,7 +170,7 @@ $convert.sex_info.sex_info_lines.__str__.strip().replace(' ','\t')#slurp
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_file" ftype="vcf" value="check.vcf" />
             <param name="convert_to"  value="gen_sample" />
             <param name="tag"  value="GT" />
@@ -182,7 +182,7 @@ $convert.sex_info.sex_info_lines.__str__.strip().replace(' ','\t')#slurp
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_file" ftype="vcf" value="convert.vcf" />
             <param name="convert_to"  value="hap_sample" />
             <output name="output_hap">
@@ -191,7 +191,7 @@ $convert.sex_info.sex_info_lines.__str__.strip().replace(' ','\t')#slurp
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input_file" ftype="vcf" value="convert.vcf" />
             <param name="convert_to"  value="hap_legend_sample" />
             <output name="output_hap">
@@ -212,7 +212,7 @@ $convert.sex_info.sex_info_lines.__str__.strip().replace(' ','\t')#slurp
             </output>
         </test>
         <!-- Test keep-duplicates option -->
-        <test>
+        <test expect_num_outputs="3">
             <param name="input_file" ftype="vcf" value="convert.vcf" />
             <param name="convert_to"  value="hap_legend_sample" />
             <param name="keep_duplicates" value="true"/>
@@ -237,7 +237,7 @@ $convert.sex_info.sex_info_lines.__str__.strip().replace(' ','\t')#slurp
             </assert_command>
         </test>
         <!-- Test region overlap -->
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_file" ftype="vcf" value="convert.vcf" />
             <param name="convert_to"  value="gen_sample" />
             <section name="sec_restrict">

diff --git a/tools/bcftools/bcftools_gtcheck.xml b/tools/bcftools/bcftools_gtcheck.xml
@@ -23,7 +23,7 @@
     bcftools index $genotypes_vcf &&
   #elif $section.genotypes.is_of_type('bcf')
     #set $genotypes_vcf = 'genotypes.bcf'
-    ln -s '$ection.genotypes' $genotypes_vcf &&
+    ln -s '$section.genotypes' $genotypes_vcf &&
     #if $section.genotypes.metadata.bcf_index:
       ln -s $section.genotypes.metadata.bcf_index ${genotypes_vcf}.csi &&
     #else

diff --git a/tools/bcftools/bcftools_plugin_color_chrs.xml b/tools/bcftools/bcftools_plugin_color_chrs.xml
@@ -67,8 +67,8 @@ bcftools plugin @EXECUTABLE@
         </section>
     </inputs>
     <outputs>
-        <data name="output_data" format="tabular" />
-        <data name="output_svg" format="svg" />
+        <data name="output_data" format="tabular" label="${tool.name} on ${on_string}: tabular" />
+        <data name="output_svg" format="svg" label="${tool.name} on ${on_string}: SVG" />
     </outputs>
     <tests>
         <test expect_num_outputs="2">

diff --git a/tools/bcftools/bcftools_stats.xml b/tools/bcftools/bcftools_stats.xml
@@ -157,13 +157,13 @@ ${section.verbose}
         </param>
     </inputs>
     <outputs>
-        <data name="output_file" format="txt"/>
-        <data name="output_pdf" format="pdf" from_work_dir="plot_tmp/summary.pdf">
+        <data name="output_file" format="txt" label="${tool.name} on ${on_string}: txt" />
+        <data name="output_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF" from_work_dir="plot_tmp/summary.pdf">
             <filter>plot_title</filter>
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_file" ftype="vcf" value="stats.b.vcf" />
             <param name="inputB_file" ftype="vcf" value="stats.a.vcf" />
             <output name="output_file">
@@ -173,7 +173,7 @@ ${section.verbose}
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_file" ftype="vcf" value="mpileup.vcf" />
             <section name="sec_default">
                 <expand macro="test_using_reference" select_from="cached" ref="mpileup" />
@@ -186,7 +186,7 @@ ${section.verbose}
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_file" ftype="vcf" value="mpileup.vcf" />
             <param name="plot_title" value="Plot for mpileup.vcf" />
             <output name="output_file">
@@ -199,7 +199,7 @@ ${section.verbose}
             <output name="output_pdf" file="summary.pdf" compare="sim_size" delta="25000" />
         </test>
         <!-- Test region overlap option-->
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_file" ftype="vcf" value="stats.b.vcf" />
             <param name="inputB_file" ftype="vcf" value="stats.a.vcf" />
             <section name="sec_restrict">
@@ -216,7 +216,7 @@ ${section.verbose}
             </assert_command>
         </test>
         <!-- Test VCF.gz input file -> REQUIRES https://github.com/galaxyproject/galaxy/pull/14605
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_file"  value="mpileup.vcf.gz" />
             <output name="output_file">
                 <assert_contents>
@@ -228,7 +228,7 @@ ${section.verbose}
         </test>
         -->
         <!-- Test modification in samples option -->
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_file" ftype="vcf" value="mpileup.vcf" />
             <section name="sec_restrict">
                 <param name="samples" value="-" />

diff --git a/tools/bcftools/macros.xml b/tools/bcftools/macros.xml
@@ -174,7 +174,7 @@ $vcfs_list_file
   </token>
 
   <xml name="macro_AF_file">
-    <param name="AF_file" argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
+    <param argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
   </xml>
   <!-- This may need to bgzip and tabix the file -->
   <token name="@PREPARE_AF_FILE@">
@@ -191,7 +191,7 @@ $vcfs_list_file
   </token>
 
   <xml name="macro_estimate_AF">
-      <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" optional="true" label="Estimate allele frequency" help="Calculate AC,AN counts on the fly, using either all samples (&quot;-&quot;) or samples listed in &lt;file&gt;" />
+      <param argument="--estimate-AF" type="data" format="data" optional="true" label="Estimate allele frequency" help="Calculate AC,AN counts on the fly, using either all samples (&quot;-&quot;) or samples listed in &lt;file&gt;" />
   </xml>
   <token name="@ESTIMATE_AF@">
 #if 'estimate_AF' in $section and $section.estimate_AF: