comparison stacks_tsv2bam.xml @ 5:a4b4bd84f69e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"

4:69842dd5aa48

<tool id="stacks2_tsv2bam" name="Stacks2: tsv2bam" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
    <description>Sort reads by RAD locus</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">

    <inputs>
        <expand macro="input_stacks_macro"/>
        <expand macro="input_cat_macro"/>
        <expand macro="input_matches_macro"/>
        <!-- TODO add BAM? -->
        <expand macro="fastq_input" fastq_optional="true" se_option="reverse reads" help="Paired end data or reverse reads. If a paired list is provided only the reverse reads are used in tsv2bam. Leave selection empty if you analyse single end data."/>
        <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M"/>
        <expand macro="in_log"/>
    </inputs>

    <outputs>

5:a4b4bd84f69e

<tool id="stacks2_tsv2bam" name="Stacks2: tsv2bam" profile="@PROFILE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>Sort reads by RAD locus</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">

    <inputs>
        <expand macro="input_stacks_macro"/>
        <expand macro="input_cat_macro"/>
        <expand macro="input_matches_macro"/>
        <!-- TODO add BAM? -->
        <expand macro="fastq_input" fastq_optional="true"  multiple="true" listtype="list:paired" se_option="reverse reads" help="Paired end data or reverse reads. If a paired list is provided only the reverse reads are used in tsv2bam. Leave selection empty if you analyse single end data."/>
        <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M"/>
        <expand macro="in_log"/>
    </inputs>

    <outputs>