comparison data_manager/salmon_index_builder.xml @ 8:ec2a1f280d67 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit 1ea9e99e1c7a7cd0f012467466e0740b6bdeb90e

7:9fc154508622

<tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.0">
    <description>index builder</description>
    <macros>
        <token name="@TOOL_VERSION@">1.3.0</token>
        <token name="@VERSION_SUFFIX@">1</token>
        <token name="@PROFILE@">24.0</token>
        <token name="@IDX_VERSION@">q7</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        ## https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/
        ## https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode
        
        #for $transcripts in $transcriptome.fields.path.split(",")
            (zcat '$transcripts' 2>/dev/null || cat '$transcripts') >> gentrome.fa &&

        salmon index
            -k $kmer_size
            -t gentrome.fa
            -d decoys.txt
            -i '$out_file.extra_files_path'
            -p "\${GALAXY_SLOTS:-12}"
            $gencode
            &&

        cp '$dmjson' '$out_file'
    ]]></command>

8:ec2a1f280d67

<tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.0">
    <description>index builder</description>
    <macros>
        <token name="@TOOL_VERSION@">1.10.1</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@PROFILE@">24.0</token>
        <token name="@IDX_VERSION@">q7</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        ## salmon uses one thread to much 
        SLOTS=\$(( \${GALAXY_SLOTS:-12} > 1 ? \${GALAXY_SLOTS:-12} - 1 : 1 ));

        ## https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/
        ## https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode
        
        #for $transcripts in $transcriptome.fields.path.split(",")
            (zcat '$transcripts' 2>/dev/null || cat '$transcripts') >> gentrome.fa &&

        salmon index
            -k $kmer_size
            -t gentrome.fa
            -d decoys.txt
            -i '$out_file.extra_files_path'
            -p "\$SLOTS"
            $gencode
            &&

        cp '$dmjson' '$out_file'
    ]]></command>