Unverified Commit e6b27a32 authored by Marius van den Beek's avatar Marius van den Beek Committed by mvdbeek
Browse files

Adjust test tool and datatype config to best practices 



Co-authored-by: default avatarBjörn Grüning <bjoern@gruenings.eu>
parent c27cec40

test/functional/tools/create_directory_index.xml

+2 −2
Original line number Diff line number Diff line 
<tool id="create_directory_index" name="Create directory index" version="1.0" profile="24.2">

    <command><![CDATA[

mkdir '$index.extra_files_path' &&

cp '$reference' '$index.extra_files_path'/1.fasta

cp '$reference' '$index.extra_files_path/1.fasta'

    ]]></command>

    <inputs>

        <param name="reference" type="data" label="Select a genome to index" help="Build an index for this FASTA sequence." format="fasta"/>
@@ -12,7 +12,7 @@ cp '$reference' '$index.extra_files_path'/1.fasta 
    <tests>

        <test>

            <param name="reference" value="1.fasta"></param>

            <output name="index">

            <output name="index" ftype="bwa_mem2_index">

                <extra_files name="1.fasta" type="file" value="1.fasta"></extra_files>

            </output>

        </test>

test/functional/tools/sample_datatypes_conf.xml

+1 −1
Original line number Diff line number Diff line
@@ -60,7 +60,7 @@ 
    </datatype>

    <datatype extension="directory" type="galaxy.datatypes.data:Directory">

    </datatype>

    <datatype extension="bwa_mem2_index" display_in_upload="true" type="galaxy.datatypes.data:Directory"/>

    <datatype extension="bwa_mem2_index" display_in_upload="true" type="galaxy.datatypes.data:Directory" subclass="true"/>

    <datatype extension="h5" type="galaxy.datatypes.binary:H5" mimetype="application/octet-stream" display_in_upload="true"/>

  </registration>

</datatypes>

test/functional/tools/use_directory_index.xml

+2 −2
Original line number Diff line number Diff line 
<tool id="use_directory_index" name="Uses directory index" version="1.0" profile="24.2">

    <command><![CDATA[

cp '$reference.extra_files_path'/1.fasta '$output'

cp '$reference.extra_files_path/1.fasta' '$output'

    ]]></command>

    <inputs>

        <param name="reference" type="data" label="Select an index" format="bwa_mem2_index"/>
@@ -10,7 +10,7 @@ cp '$reference.extra_files_path'/1.fasta '$output' 
    </outputs>

    <tests>

        <test>

            <param name="reference" value="bwa_mem2_index" class="Directory"></param>

            <param name="reference" value="bwa_mem2_index" class="Directory" ftype="bwa_mem2_index"></param>

            <output name="output" value="1.fasta" />

        </test>

    </tests>