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Add new tool gene.iobio #5365

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merged 12 commits into from
Jun 29, 2023
Merged

Add new tool gene.iobio #5365

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9a58c95
Add gene.iobio
JasperO98 Jun 20, 2023
c307232
Create .shed.yml
JasperO98 Jun 20, 2023
d6015ae
Update version and tool name
JasperO98 Jun 20, 2023
3a37299
add tests
JasperO98 Jun 21, 2023
57f77c1
add test-data
JasperO98 Jun 21, 2023
3d9361b
add warning data transfer
JasperO98 Jun 21, 2023
0e4a78a
update warning
JasperO98 Jun 21, 2023
73e1bfd
update description
JasperO98 Jun 21, 2023
7ff5832
fix linting
JasperO98 Jun 21, 2023
d0cd1f9
update test output check
JasperO98 Jun 21, 2023
ceea879
reduce bam sizes to 1mb
JasperO98 Jun 21, 2023
d10ac65
fix bams
JasperO98 Jun 21, 2023
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10 changes: 10 additions & 0 deletions tools/geneiobio/.shed.yml
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name: geneiobio
owner: iuc
categories:
- Sequence Analysis
description: Gene.iobio is an interactive tool for variant and trio analysis.
long_description: |
Gene.iobio is an interactive tool for variant and trio analysis.
remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio
homepage_url: https://github.com/iobio/gene.iobio
type: unrestricted
169 changes: 169 additions & 0 deletions tools/geneiobio/geneiobio-iframe.xml
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<tool id="gene_iobio_display_generation_iframe" name="gene.iobio visualisation" version="4.7.1">
<description>analyses VCFs for single and trio analysis to find causative variants using gene.iobio's public server</description>
<command>cat '$index' | tr -d '\n' > '$outfile'</command>
<configfiles>
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<configfile name="index"><![CDATA[
<html>
<body>
<iframe src="https://gene.iobio.io/?genes=${genes}
&species=Human
&build=${refgen_version}
&affectedSibs=
&unaffectedSibs=
&rel0=proband
&sex0=${proband_sex}
&vcf0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_vcf.id)}/display
&tbi0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_vcf.id)}/metadata_file%3Fmetadata_file%3Dtabix_index
#if $proband_bam.ext == 'bam':
&bam0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/display
&bai0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/metadata_file%3Fmetadata_file%3Dbam_index
#elif $proband_bam.ext == 'cram':
&cram0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/display
&cai0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/metadata_file%3Fmetadata_file%3Dcram_index
#end if
&sample0=${proband_name}
&affectedStatus0=${proband_affected}
#if str( $input_type.input_type_selector ) == "trio"#
&rel1=father
&sex1=male
&vcf1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.vcf.id)}/display
&tbi1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.vcf.id)}/metadata_file%3Fmetadata_file%3Dtabix_index
#if $input_type.father.bam.ext == 'bam':
&bam1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/display
&bai1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/metadata_file%3Fmetadata_file%3Dbam_index
#elif $input_type.father.bam.ext == 'cram':
&cram1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/display
&cai1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/metadata_file%3Fmetadata_file%3Dcram_index
#end if
&sample1=${input_type.father.name}
&affectedStatus1=${input_type.father.affected}
&rel2=mother
&sex2=female
&vcf2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.vcf.id)}/display
&tbi2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.vcf.id)}/metadata_file%3Fmetadata_file%3Dtabix_index
#if $input_type.mother.bam.ext == 'bam':
&bam2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/display
&bai2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/metadata_file%3Fmetadata_file%3Dbam_index
#elif $input_type.mother.bam.ext == 'cram':
&cram2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/display
&cai2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/metadata_file%3Fmetadata_file%3Dcram_index
#end if
&sample2=${input_type.mother.name}
&affectedStatus2=${input_type.mother.affected}
#end if
" style="width: 100%; height: 900px;"></iframe>
</body></html>
]]></configfile>
</configfiles>
<inputs>
<param name="proband_vcf" type="data" format="vcf,vcf_bgzip" label="Proband VCF file"/>
<param name="proband_bam" type="data" format="bam,cram" label="Proband BAM file" optional="true"/>
<param name="proband_sex" type="select" display="radio" label="Proband sex">
<option value="male" selected="true">Male</option>
<option value="female">Female</option>
</param>
<param name="proband_affected" type="boolean" truevalue="affected" falsevalue="unaffected" checked="true" label="Is the proband affected?"/>
<param name="proband_name" type="text" value="C" label="Proband sample name" help="The sample names are listed in the columns of the VCF."/>
<conditional name="input_type">
<param name="input_type_selector" type="select" display="radio" label="Single/Trio analysis">
<option value="single" selected="true">Single</option>
<option value="trio">Trio</option>
</param>
<when value="trio">
<section name="father" title="Father input">
<param name="vcf" type="data" format="vcf,vcf_bgzip" label="Father VCF file"/>
<param name="bam" type="data" format="bam,cram" label="Father BAM file" optional="true"/>
<param name="affected" type="boolean" truevalue="affected" falsevalue="unaffected" checked="false" label="Is the father affected?"/>
<param name="name" type="text" value="F" label="Father sample name" help="The sample names are listed in the columns of the VCF."/>
</section>
<section name="mother" title="Mother input">
<param name="vcf" type="data" format="vcf,vcf_bgzip" label="Mother VCF file"/>
<param name="bam" type="data" format="bam,cram" label="Mother BAM file" optional="true"/>
<param name="affected" type="boolean" truevalue="affected" falsevalue="unaffected" checked="false" label="Is the mother affected?"/>
<param name="name" type="text" value="M" label="Mother sample name" help="The sample names are listed in the columns of the VCF."/>
</section>
</when>
<when value="single">
</when>
</conditional>
<param name="genes" type="text" value="PDHA1,ARHGAP8,RAI1,PLXNA1,SCN8A,SMARCA2" size="100x5" label="Genes of interest" help="Provide the genes as a comma seperated line. This line can be empty and genes can be selected interactively using gene.iobio."/>
<param name="refgen_version" type="select" label="Select reference genome version">
<option value="GRCh38" selected="true">GRCh38</option>
<option value="GRCh37">GRCh37</option>
</param>
</inputs>
<outputs>
<data name="outfile" format="html" />
</outputs>
<tests>
<!-- Test 1 - Single -->
<test expect_num_outputs="1">
<param name="proband_vcf" ftype="vcf" value="family.vcf.gz"/>
<param name="proband_bam" ftype="bam" value="proband.bam" />
<param name="proband_sex" ftype="text" value="female" />
<param name="proband_name" ftype="text" value="Case5C" />
<param name="genes" ftype="text" value="BRCA1" />
<param name="refgen_version" ftype="text" value="GRCh37" />
<output name="outfile">
<assert_contents>
<has_size value= "659" delta="100" />
</assert_contents>
</output>
</test>
<!-- Test 2 - Trio -->
<test expect_num_outputs="1">
<param name="proband_vcf" ftype="vcf" value="family.vcf.gz"/>
<param name="proband_bam" ftype="bam" value="proband.bam" />
<param name="proband_sex" ftype="text" value="female" />
<param name="proband_name" ftype="text" value="Case5C" />
<param name="genes" ftype="text" value="BRCA1" />
<param name="refgen_version" ftype="text" value="GRCh37" />
<conditional name="input_type">
<param name="input_type_selector" value="trio"/>
<section name="mother">
<param name="vcf" ftype="vcf" value="family.vcf.gz"/>
<param name="bam" ftype="bam" value="mother.bam" />
<param name="affected" ftype="text" value="affected" />
<param name="name" ftype="text" value="Case5M" />
</section>
<section name="father">
<param name="vcf" ftype="vcf" value="family.vcf.gz"/>
<param name="bam" ftype="bam" value="father.bam" />
<param name="affected" ftype="text" value="unaffected" />
<param name="name" ftype="text" value="Case5F" />
</section>
</conditional>
<output name="outfile">
<assert_contents>
<has_size value= "1555" delta="500" />
</assert_contents>
</output>
</test>
</tests>
<help><![CDATA[
Gene.iobio provides a report of impactful variants. Gene.iobio also helps prioritize variants based on multiple integrated gene:disease association algorithms and knowledge bases.
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I guess we should be very clear that data is transferred to their servers, since maybe with an iframe it isn't immediately obvious. We could add a warning in the help text

.. class:: Warning mark

This transfers data to a remote server, in US jurisdiction

(with the correct indentation of course)

alternatively maybe that could be a mandatory checkbox that the user has to check to acknowledge? I just worry with such a useful tool for human data someone makes a mistake a bit.

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But in order to use the tool you'd need to make the history public right? I would say that's quite clear, but indeed we'll need to mention it here

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yes, that's true, we don't mention that somewhere, we should mention that as well.


.. class:: Warning mark

This transfers data to a remote server, in US jurisdiction. In order to do this make sure to make the history accessible, i.e. anyone with a link can reach the data.

Required inputs:

1. Proband VCF file

Optional inputs (trio analysis):

1. Proband BAM file
2. Father & Mother BAM file
3. Father & Mother VCF file

The `iobio project`_ is developed by the `Marth lab`_ at the `University of Utah Center for Genetic Discovery`_.

.. _iobio project: https://iobio.io
.. _Marth lab: https://marthlab.org/
.. _University of Utah Center for Genetic Discovery: https://ucgd.genetics.utah.edu/
]]></help>
<citations>
<citation type="doi">10.1038/s41598-021-99752-5</citation>
</citations>
</tool>
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