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comparison geneiobio-iframe.xml @ 1:c24c1506cb8d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit fab39612473d91e048868d9c122d7dd61a2bd9d4
author iuc
date Mon, 24 Jul 2023 16:06:43 +0000
parents 0922887dfe47
children
comparison
equal deleted inserted replaced
0:0922887dfe47 1:c24c1506cb8d
1 <tool id="gene_iobio_display_generation_iframe" name="gene.iobio visualisation" version="4.7.1"> 1 <tool id="gene_iobio_display_generation_iframe" name="gene.iobio visualisation" version="4.7.1+galaxy1">
2 <description>analyses VCFs for single and trio analysis to find causative variants using gene.iobio's public server</description> 2 <description>analyses VCFs for single and trio analysis to find causative variants using gene.iobio's public server</description>
3 <command>cat '$index' | tr -d '\n' > '$outfile'</command> 3 <command>cat '$index' | tr -d '\n' > '$outfile'</command>
4 <configfiles> 4 <configfiles>
5 <configfile name="index"><![CDATA[ 5 <configfile name="index"><![CDATA[
6 <html> 6 <html>
54 " style="width: 100%; height: 900px;"></iframe> 54 " style="width: 100%; height: 900px;"></iframe>
55 </body></html> 55 </body></html>
56 ]]></configfile> 56 ]]></configfile>
57 </configfiles> 57 </configfiles>
58 <inputs> 58 <inputs>
59 <param name="proband_vcf" type="data" format="vcf,vcf_bgzip" label="Proband VCF file"/> 59 <param name="proband_vcf" type="data" format="vcf_bgzip" label="Proband VCF file"/>
60 <param name="proband_bam" type="data" format="bam,cram" label="Proband BAM file" optional="true"/> 60 <param name="proband_bam" type="data" format="bam,cram" label="Proband BAM file" optional="true"/>
61 <param name="proband_sex" type="select" display="radio" label="Proband sex"> 61 <param name="proband_sex" type="select" display="radio" label="Proband sex">
62 <option value="male" selected="true">Male</option> 62 <option value="male" selected="true">Male</option>
63 <option value="female">Female</option> 63 <option value="female">Female</option>
64 </param> 64 </param>
69 <option value="single" selected="true">Single</option> 69 <option value="single" selected="true">Single</option>
70 <option value="trio">Trio</option> 70 <option value="trio">Trio</option>
71 </param> 71 </param>
72 <when value="trio"> 72 <when value="trio">
73 <section name="father" title="Father input"> 73 <section name="father" title="Father input">
74 <param name="vcf" type="data" format="vcf,vcf_bgzip" label="Father VCF file"/> 74 <param name="vcf" type="data" format="vcf_bgzip" label="Father VCF file"/>
75 <param name="bam" type="data" format="bam,cram" label="Father BAM file" optional="true"/> 75 <param name="bam" type="data" format="bam,cram" label="Father BAM file" optional="true"/>
76 <param name="affected" type="boolean" truevalue="affected" falsevalue="unaffected" checked="false" label="Is the father affected?"/> 76 <param name="affected" type="boolean" truevalue="affected" falsevalue="unaffected" checked="false" label="Is the father affected?"/>
77 <param name="name" type="text" value="F" label="Father sample name" help="The sample names are listed in the columns of the VCF."/> 77 <param name="name" type="text" value="F" label="Father sample name" help="The sample names are listed in the columns of the VCF."/>
78 </section> 78 </section>
79 <section name="mother" title="Mother input"> 79 <section name="mother" title="Mother input">
80 <param name="vcf" type="data" format="vcf,vcf_bgzip" label="Mother VCF file"/> 80 <param name="vcf" type="data" format="vcf_bgzip" label="Mother VCF file"/>
81 <param name="bam" type="data" format="bam,cram" label="Mother BAM file" optional="true"/> 81 <param name="bam" type="data" format="bam,cram" label="Mother BAM file" optional="true"/>
82 <param name="affected" type="boolean" truevalue="affected" falsevalue="unaffected" checked="false" label="Is the mother affected?"/> 82 <param name="affected" type="boolean" truevalue="affected" falsevalue="unaffected" checked="false" label="Is the mother affected?"/>
83 <param name="name" type="text" value="M" label="Mother sample name" help="The sample names are listed in the columns of the VCF."/> 83 <param name="name" type="text" value="M" label="Mother sample name" help="The sample names are listed in the columns of the VCF."/>
84 </section> 84 </section>
85 </when> 85 </when>