comparison data_manager/rna_star_index_builder.xml @ 6:64deddb6a8ec draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"

5:f5eb9afa8f8a

<tool id="rna_star_index_builder_data_manager" name="rnastar index2" tool_type="manage_data" version="2.7.1a" profile="17.01">
    <description>builder</description>

    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements" />

    <command><![CDATA[
if [ -z "\$GALAXY_MEMORY_MB" ] ; then
    GALAXY_MEMORY_BYTES=31000000000 ;
else
    GALAXY_MEMORY_BYTES=\$((GALAXY_MEMORY_MB * 1000000)) ;
fi ;

#import json, os
#set params = json.loads(open(str($out_file)).read())
#set target_directory = $params['output_data'][0]['extra_files_path'].encode('ascii', 'replace')
#set subdir = os.path.basename(target_directory)

mkdir -p '${target_directory}/${subdir}' &&

STAR
--runMode genomeGenerate
--genomeFastaFiles '${all_fasta_source.fields.path}'
--genomeDir '${target_directory}/${subdir}'
--limitGenomeGenerateRAM \${GALAXY_MEMORY_BYTES}
#if $GTFconditional.GTFselect == "withGTF":
    --sjdbGTFfile '${GTFconditional.sjdbGTFfile}'
    --sjdbOverhang ${GTFconditional.sjdbOverhang}
#end if

    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>

    <!-- not available in planemo at the moment of writing
    <tests>
        <test>
            <param name="all_fasta_source" value="phiX.fa"/>
            <param name="sequence_name" value="phiX"/>
            <param name="sequence_id" value="minimal-settings"/>
            <param name="modelformat" value="None"/>

            <output name="out_file" file="test_star_01.data_manager_json"/>
        </test>
    </tests>
    -->

    <help><![CDATA[
.. class:: infomark

*What it does*

This is a Galaxy datamanager for the rna STAR gap-aware RNA aligner.

Please read the fine manual - that and the google group are the places to learn about the options above.

*Memory requirements*

6:64deddb6a8ec

<tool id="rna_star_index_builder_data_manager" name="rnastar index2" tool_type="manage_data" version="@IDX_VERSION@+galaxy2" profile="19.05">
    <description>builder</description>

    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements">
        <requirement type="package" version="3.7">python</requirement>
    </expand>

    <command><![CDATA[
if [ -z "\$GALAXY_MEMORY_MB" ] ; then
    GALAXY_MEMORY_BYTES=31000000000 ;
else
    GALAXY_MEMORY_BYTES=\$((GALAXY_MEMORY_MB * 1000000)) ;
fi ;

#import os
#set $target_directory = str($out_file.extra_files_path)
#set $subdir = os.path.basename($target_directory)

mkdir '${target_directory}' &&

STAR
--runMode genomeGenerate
--genomeFastaFiles '${all_fasta_source.fields.path}'
--genomeDir '${target_directory}'
--limitGenomeGenerateRAM \${GALAXY_MEMORY_BYTES}
#if $GTFconditional.GTFselect == "withGTF":
    --sjdbGTFfile '${GTFconditional.sjdbGTFfile}'
    --sjdbOverhang ${GTFconditional.sjdbOverhang}
#end if

    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>

    <tests>
        <test>
            <param name="all_fasta_source" value="phiX174"/>
            <param name="sequence_name" value="phiX"/>
            <param name="sequence_id" value="minimal-settings"/>
            <param name="modelformat" value="None"/>

            <output name="out_file" file="test_star_01.data_manager_json" compare="re_match"/>
        </test>
    </tests>

    <help><![CDATA[
.. class:: infomark

*What it does*

This is a Galaxy data manager tool for the gap-aware RNA aligner STAR.

This version of the tool builds STAR indices of the format first introduced
with STAR version @IDX_VERSION@.

Please read the fine manual - that and the google group are the places to learn about the options above.

*Memory requirements*