annotate data_manager/bowtie2_index_builder.xml @ 12:6754002631cd draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit e5971e34b23280f7c3d6291a03325b6dd47e3fdd

<tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
    <description>builder</description>
    <macros>
        <token name="@WRAPPER_VERSION@">2.5.4</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@WRAPPER_VERSION@">bowtie2</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #set $value = $sequence_id or $all_fasta_source.fields.dbkey
        #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
        mkdir -p '${out_file.extra_files_path}' &&
        ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' &&
        cd '${out_file.extra_files_path}' &&
        bowtie2-build --threads \${GALAXY_SLOTS:-1} '${out_file.extra_files_path}/${fasta_file_name}' '${value}' &&
        rm '${out_file.extra_files_path}/${fasta_file_name}' &&
        cp '$dmjson' '$out_file'
    ]]></command>
    <configfiles>
        <configfile name="dmjson"><![CDATA[#slurp
#set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
#set $value = $sequence_id or $all_fasta_source.fields.dbkey
#set $name = $sequence_name or $all_fasta_source.fields.name
{
  "data_tables":{
    "bowtie2_indexes":[
      {
        "value": "${value}",
        "dbkey": "${all_fasta_source.fields.dbkey}",
        "name": "${name}",
        "path": "${value}"
      }
#if $tophat2:
    ],
    "tophat2_indexes":[
      {
        "value": "${value}",
        "dbkey": "${all_fasta_source.fields.dbkey}",
        "name": "${name}",
        "path": "${value}"
      }
#end if
    ]
  }
}
]]></configfile>
    </configfiles>
    <inputs>
        <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
            <options from_data_table="all_fasta"/>
        </param>
        <param name="sequence_name" type="text" value="" label="Name of sequence" />
        <param name="sequence_id" type="text" value="" label="ID for sequence" />
        <param name="tophat2" type="boolean" checked="True" label="Also make available for TopHat" help="Adds values to tophat2_indexes tool data table" />
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <param name="all_fasta_source" value="phiX174"/>
            <output name="out_file" value="bowtie2_data_manager.1.json"/>
        </test>
        <test>
            <param name="all_fasta_source" value="phiX174"/>
            <param name="sequence_name" value="Galeocerdo cuvier"/>
            <param name="sequence_id" value="tigHai1"/>
            <param name="tophat2" value="False"/>
            <output name="out_file" file="bowtie2_data_manager.2.json"/>
        </test>
    </tests>

    <help>
.. class:: infomark

**Notice:** If you leave name, description, or id blank, it will be generated automatically.
    </help>
</tool>