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changeset 0:c0af7b196a89 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
author iuc
date Thu, 29 Jun 2023 08:33:46 +0000
parents
children fc53fcdbe548
files geneiobio-iframe.xml test-data/family.vcf.gz test-data/father.bam test-data/mother.bam test-data/proband.bam
diffstat 5 files changed, 169 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/geneiobio-iframe.xml	Thu Jun 29 08:33:46 2023 +0000
@@ -0,0 +1,169 @@
+<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>
+		<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.
+	
+	.. 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>
Binary file test-data/family.vcf.gz has changed
Binary file test-data/father.bam has changed
Binary file test-data/mother.bam has changed
Binary file test-data/proband.bam has changed