comparison gemini_set_somatic.xml @ 5:991049484627 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59

4:7b031989ea12

<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
    <description>Tag somatic mutations in a GEMINI database</description>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">set_somatic</token>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        cp "${ infile }" "${ outfile }" &&

        gemini @BINARY@

        #if float($min_depth) >= 0:
            --min-depth $min_depth

        #if int($min_tumor_depth) >= 0:
            --min-tumor-depth $min_tumor_depth
        #end if

        #if str($chrom).strip():
            --chrom "$chrom"
        #end if 
        "${ outfile }"
]]>
    </command>
    <inputs>

        <expand macro="infile" />

5:991049484627

<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
    <description>Tag somatic mutations in a GEMINI database</description>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">set_somatic</token>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        cp '$infile' '$outfile' &&

        gemini @BINARY@

        #if float($min_depth) >= 0:
            --min-depth $min_depth

        #if int($min_tumor_depth) >= 0:
            --min-tumor-depth $min_tumor_depth
        #end if

        #if str($chrom).strip():
            --chrom '$chrom'
        #end if 
        '$outfile'
]]>
    </command>
    <inputs>

        <expand macro="infile" />