comparison stacks_gstacks.xml @ 1:192f1d5f301e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty

0:ce90584be117

<tool id="stacks2_gstacks" name="Stacks2: gstacks" version="@WRAPPER_VERSION@">
    <description>match stacks to a catalog</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

        #set count = len($input_type.input_bam)
    #else
        #set count = len($input_type.input_bam.keys())
    #end if
    #if count == 1:
        #for $bam in $input_type.input_bam:
            ln -s '$bam' bam_inputs/catalog.bam && 
        #end for
    #else
        >&2 echo "exactly one (merged) bam file is needed in denovo mode if no population map is given" &&
        exit 1 &&

    </outputs>

    <tests>
        <!-- denovomode, w popmap -->
        <test>
            <param name="input_type|input_type_selector" value="list"/>
            <param name="input_type|input_bam">
                <collection type="list">
                    <element name="PopA_01.matches" ftype="bam" value="tsv2bam/PopA_01.matches.bam" />
                    <element name="PopA_02.matches" ftype="bam" value="tsv2bam/PopA_02.matches.bam" />
               </collection>
            </param>

                <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" compare="sim_size"/>
            </output_collection>
        </test>
        <!-- denovomode, wo popmap (allows for only one input), ignore PE, advanced, alt model -->
        <test>
            <param name="input_type|input_type_selector" value="manual"/>
            <param name="input_type|input_bam" value="tsv2bam/PopA_01.matches.bam" ftype="bam"/>
            <conditional name="mode_cond">
                <param name="mode_select" value="denovo" />
                <param name="ignore_pe_reads" value="--ignore-pe-reads" />
                <conditional name="advanced_cond">
                    <param name="advanced_select" value="yes"/>

            <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output>
            <output_collection name="gstacks_out" type="list" count="2"/>
        </test>
        <!-- refbased wo popmap, paired options, removing all unpaired reads results in an error -->
        <test expect_failure="true" expect_exit_code="1">
            <param name="input_type|input_type_selector" value="manual"/>
            <param name="input_type|input_bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/>
            <conditional name="mode_cond">
                <param name="mode_select" value="refbased"/>
                <conditional name="paired_cond">
                    <param name="paired_select" value=""/>
                    <!--<param name="rm_unpaired_reads" value="\-\-rm-unpaired-reads" /> removes to much of the test data and gstacks fails-->

                <has_text text="--rm-pcr-duplicates" />
            </assert_command>
        </test>
        <!-- refbased w popmap (here bam names need to be equal to sample names in popmap), \-\-unpaired, advanced, snp model -->
        <test>
            <param name="input_type|input_type_selector" value="list"/>
            <param name="input_type|input_bam">
                <collection type="list">
                    <element name="PopA_01" ftype="bam" value="tsv2bam/PopA_01.matches.bam" />
                    <element name="PopA_02" ftype="bam" value="tsv2bam/PopA_02.matches.bam" />
               </collection>
            </param>

            <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output>
            <output_collection name="gstacks_out" type="list" count="2"/>
        </test>
        <!-- refbased wo popmap (here bam names don't matter), \-\-ignorepe -->
        <test>
            <param name="input_type|input_type_selector" value="list"/>
            <param name="input_type|input_bam">
                <collection type="list">
                    <element name="PopA_01.matches" ftype="bam" value="tsv2bam/PopA_01.matches.bam" />
                    <element name="PopA_02.matches" ftype="bam" value="tsv2bam/PopA_02.matches.bam" />
               </collection>
            </param>

1:192f1d5f301e

<tool id="stacks2_gstacks" name="Stacks2: gstacks" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
    <description>match stacks to a catalog</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

        #set count = len($input_type.input_bam)
    #else
        #set count = len($input_type.input_bam.keys())
    #end if
    #if count == 1:
        #for $bam in $input_bam:
            ln -s '$bam' bam_inputs/catalog.bam && 
        #end for
    #else
        >&2 echo "exactly one (merged) bam file is needed in denovo mode if no population map is given" &&
        exit 1 &&

    </outputs>

    <tests>
        <!-- denovomode, w popmap -->
        <test>
            <param name="input_bam">
                <collection type="list">
                    <element name="PopA_01.matches" ftype="bam" value="tsv2bam/PopA_01.matches.bam" />
                    <element name="PopA_02.matches" ftype="bam" value="tsv2bam/PopA_02.matches.bam" />
               </collection>
            </param>

                <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" compare="sim_size"/>
            </output_collection>
        </test>
        <!-- denovomode, wo popmap (allows for only one input), ignore PE, advanced, alt model -->
        <test>
            <param name="input_bam" value="tsv2bam/PopA_01.matches.bam" ftype="bam"/>
            <conditional name="mode_cond">
                <param name="mode_select" value="denovo" />
                <param name="ignore_pe_reads" value="--ignore-pe-reads" />
                <conditional name="advanced_cond">
                    <param name="advanced_select" value="yes"/>

            <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output>
            <output_collection name="gstacks_out" type="list" count="2"/>
        </test>
        <!-- refbased wo popmap, paired options, removing all unpaired reads results in an error -->
        <test expect_failure="true" expect_exit_code="1">
            <param name="input_bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/>
            <conditional name="mode_cond">
                <param name="mode_select" value="refbased"/>
                <conditional name="paired_cond">
                    <param name="paired_select" value=""/>
                    <!--<param name="rm_unpaired_reads" value="\-\-rm-unpaired-reads" /> removes to much of the test data and gstacks fails-->

                <has_text text="--rm-pcr-duplicates" />
            </assert_command>
        </test>
        <!-- refbased w popmap (here bam names need to be equal to sample names in popmap), \-\-unpaired, advanced, snp model -->
        <test>
            <param name="input_bam">
                <collection type="list">
                    <element name="PopA_01" ftype="bam" value="tsv2bam/PopA_01.matches.bam" />
                    <element name="PopA_02" ftype="bam" value="tsv2bam/PopA_02.matches.bam" />
               </collection>
            </param>

            <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output>
            <output_collection name="gstacks_out" type="list" count="2"/>
        </test>
        <!-- refbased wo popmap (here bam names don't matter), \-\-ignorepe -->
        <test>
            <param name="input_bam">
                <collection type="list">
                    <element name="PopA_01.matches" ftype="bam" value="tsv2bam/PopA_01.matches.bam" />
                    <element name="PopA_02.matches" ftype="bam" value="tsv2bam/PopA_02.matches.bam" />
               </collection>
            </param>