comparison bowtie2_wrapper.xml @ 24:017aba02828d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac

23:17062a0decb7

<tool id="bowtie2" name="Bowtie2" version="2.3.4.2" profile="18.01">
    <description>- map reads against reference genome</description>
    <macros>
        <import>bowtie2_macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="2.3.4">bowtie2</requirement>
        <requirement type="package" version="1.8">samtools</requirement>
    </requirements>
    <version_command>bowtie2 --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
## Use pipefail if available to quit with first non-zero exit code
set -o | grep -q pipefail && set -o pipefail;

#if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''):
    | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$output'
#else if $sam_options.reorder:
    | samtools view -bS - -o '$output'
#else:
    > '$output_sam'
#end if

## rename unaligned sequence files
#if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
    #from os.path import splitext

                    </when>
                </conditional>
                <expand macro="dbKeyActions" />
            </actions>
        </data>
        <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (BAM)">
          <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter>
          <change_format>
              <when input="sam_options.reorder" value="--reorder" format="qname_input_sorted.bam" />
          </change_format>
          <actions>
            <conditional name="reference_genome.source">
              <when value="indexed">
                <action type="metadata" name="dbkey">
                  <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
                    <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                    <filter type="param_value" ref="reference_genome.index" column="0"/>
                  </option>
                </action>
              </when>
              <when value="history">
                <action type="metadata" name="dbkey">
                  <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
                </action>
              </when>
            </conditional>
            <expand macro="dbKeyActions" />
          </actions>
        </data>
        <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)">
          <filter>analysis_type['analysis_type_selector'] == "full" and analysis_type['sam_opt'] is True</filter>
          <actions>
            <conditional name="reference_genome.source">
              <when value="indexed">
                <action type="metadata" name="dbkey">
                  <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">

            <expand macro="dbKeyActions" />
          </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <!-- test on paired-end datasets -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>
            <param name="unaligned_file" value="false"/>
            <param name="analysis_type_selector" value="simple"/>

            <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
            <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test>
            <!-- test on paired collection -->
            <param name="type" value="paired_collection"/>
            <param name="paired_options_selector" value="no"/>
            <param name="unaligned_file" value="false"/>
            <param name="analysis_type_selector" value="simple"/>

                </collection>
            </param>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test>
            <!-- test on paired-end datasets with read group info -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>
            <param name="unaligned_file" value="false"/>
            <param name="analysis_type_selector" value="simple"/>

            <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
            <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test>
            <!-- test on paired-end datasets with stats output -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>
            <param name="unaligned_file" value="false"/>
            <param name="analysis_type_selector" value="simple"/>

                <assert_contents>
                    <has_text text="of these" />
                </assert_contents>
            </output>
        </test>
        <test>
            <!-- test on interleaved dataset -->
            <param name="type" value="paired_interleaved"/>
            <!-- <param name="paired_options_selector" value="no"/> -->
            <param name="unaligned_file" value="false"/>
            <param name="analysis_type_selector" value="simple"/>

            <param name="source" value="history" />
            <param name="input_1" value="bowtie2-fq_il.fq" ftype="fastqsanger"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test>
            <!-- test on fastqsanger.gz paired-end datasets -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>
            <param name="unaligned_file" value="false"/>
            <param name="analysis_type_selector" value="simple"/>

            <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/>
            <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test>
            <!-- test on fastqsanger.bz2 paired-end datasets -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>
            <param name="unaligned_file" value="false"/>
            <param name="analysis_type_selector" value="simple"/>

            <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/>
            <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test>
            <!-- test on fasta paired-end datasets -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>
            <param name="unaligned_file" value="false"/>
            <param name="analysis_type_selector" value="simple"/>

            <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
            <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test>
            <!-- test on fasta paired-end datasets with bam_native as output -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>
            <param name="unaligned_file" value="false"/>
            <param name="analysis_type_selector" value="simple"/>

            <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <param name="sam_options_selector" value="yes" />
            <param name="reorder" value="true" />
            <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
**Bowtie2 Overview**

24:017aba02828d

<tool id="bowtie2" name="Bowtie2" version="2.3.4.3" profile="18.01">
    <description>- map reads against reference genome</description>
    <macros>
        <import>bowtie2_macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="2.3.4.1">bowtie2</requirement>
        <requirement type="package" version="1.9">samtools</requirement>
    </requirements>
    <version_command>bowtie2 --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
## Use pipefail if available to quit with first non-zero exit code
set -o | grep -q pipefail && set -o pipefail;

#if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''):
    | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$output'
#else if $sam_options.reorder:
    | samtools view -bS - -o '$output'
#else:
    > '$output'
#end if

## rename unaligned sequence files
#if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
    #from os.path import splitext

                    </when>
                </conditional>
                <expand macro="dbKeyActions" />
            </actions>
        </data>
        <data format="bam" name="output" label="${tool.name} on ${on_string}: alignments">
          <change_format>
              <when input="sam_options.reorder" value="--reorder" format="qname_input_sorted.bam" />
              <when input="sam_options.sam_opt" value="true" format="sam" />
          </change_format>
          <actions>
            <conditional name="reference_genome.source">
              <when value="indexed">
                <action type="metadata" name="dbkey">
                  <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">

            <expand macro="dbKeyActions" />
          </actions>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <!-- test on paired-end datasets -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>
            <param name="unaligned_file" value="false"/>
            <param name="analysis_type_selector" value="simple"/>

            <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
            <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test expect_num_outputs="1">
            <!-- test on paired collection -->
            <param name="type" value="paired_collection"/>
            <param name="paired_options_selector" value="no"/>
            <param name="unaligned_file" value="false"/>
            <param name="analysis_type_selector" value="simple"/>

                </collection>
            </param>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test expect_num_outputs="1">
            <!-- test on paired-end datasets with read group info -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>
            <param name="unaligned_file" value="false"/>
            <param name="analysis_type_selector" value="simple"/>

            <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
            <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test on paired-end datasets with stats output -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>
            <param name="unaligned_file" value="false"/>
            <param name="analysis_type_selector" value="simple"/>

                <assert_contents>
                    <has_text text="of these" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <!-- test on interleaved dataset -->
            <param name="type" value="paired_interleaved"/>
            <!-- <param name="paired_options_selector" value="no"/> -->
            <param name="unaligned_file" value="false"/>
            <param name="analysis_type_selector" value="simple"/>

            <param name="source" value="history" />
            <param name="input_1" value="bowtie2-fq_il.fq" ftype="fastqsanger"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test expect_num_outputs="1">
            <!-- test on fastqsanger.gz paired-end datasets -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>
            <param name="unaligned_file" value="false"/>
            <param name="analysis_type_selector" value="simple"/>

            <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/>
            <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test expect_num_outputs="1">
            <!-- test on fastqsanger.bz2 paired-end datasets -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>
            <param name="unaligned_file" value="false"/>
            <param name="analysis_type_selector" value="simple"/>

            <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/>
            <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test expect_num_outputs="1">
            <!-- test on fasta paired-end datasets -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>
            <param name="unaligned_file" value="false"/>
            <param name="analysis_type_selector" value="simple"/>

            <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
            <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test expect_num_outputs="1">
            <!-- test on fasta paired-end datasets with bam_native as output -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>
            <param name="unaligned_file" value="false"/>
            <param name="analysis_type_selector" value="simple"/>

            <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <param name="sam_options_selector" value="yes" />
            <param name="reorder" value="true" />
            <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" compare="sim_size"/>
        </test>
        <test expect_num_outputs="1">
            <!-- test on fasta paired-end datasets with sam as output -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>
            <param name="unaligned_file" value="false"/>
            <param name="analysis_type_selector" value="simple"/>
            <param name="source" value="history" />
            <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
            <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <param name="sam_options_selector" value="yes" />
            <param name="sam_options|sam_opt" value="true" />
            <output name="output" ftype="sam">
                <assert_contents>
                    <has_text text="M01368:8:000000000-A3GHV:1:1101:6911:8255" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**Bowtie2 Overview**