Mercurial > repos > iuc > geneiobio
comparison geneiobio-iframe.xml @ 1:fc53fcdbe548 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit fab39612473d91e048868d9c122d7dd61a2bd9d4
| author | iuc |
|---|---|
| date | Mon, 24 Jul 2023 16:06:54 +0000 |
| parents | c0af7b196a89 |
| children |
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| 0:c0af7b196a89 | 1:fc53fcdbe548 |
|---|---|
| 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> |