Mercurial > repos > public-health-bioinformatics > micall_lite
diff micall_lite.xml @ 3:786c437c144c draft
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
| author | public-health-bioinformatics |
|---|---|
| date | Thu, 27 Feb 2020 19:15:39 -0500 |
| parents | e5390c4b69e9 |
| children |
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--- a/micall_lite.xml Wed Jan 08 19:36:00 2020 -0500 +++ b/micall_lite.xml Thu Feb 27 19:15:39 2020 -0500 @@ -1,5 +1,7 @@ <tool id="micall_lite" name="micall_lite" version="@TOOL_VERSION@+galaxy0"> - <description></description> + <description> + Human RNA virus genotyping pipeline + </description> <macros> <import>macros.xml</import> </macros> @@ -46,14 +48,21 @@ #end if mkdir 'outdir' && + micall --threads \${GALAXY_SLOTS:-1} + --keep #if $unzipped: --unzipped #end if --readlen ${readlen} '${reads1}' '${reads2}' + #if str( $projects_file_source.projects_file_source_selector ) == "tool_data_table": + --projects '${projects_file_source.projects_file.fields.path}' + #elif str( $projects_file_source.projects_file_source_selector ) == 'history': + --projects '${projects_file_source.projects_file}' + #end if --outdir 'outdir' ]]> </command> @@ -71,6 +80,25 @@ <param format="@INTYPES@" name="pair" type="data_collection" collection_type="paired" label="Collection of paired reads"/> </when> </conditional> + <conditional name="projects_file_source"> + <param name="projects_file_source_selector" type="select" + label="Select a projects file from your history or use one from a tool data table?"> + <option value="none" selected="true">No projects file</option> + <option value="tool_data_table">Projects file from tool data table</option> + <option value="history">Projects file from history</option> + </param> + <when value="none"/> + <when value="tool_data_table"> + <param name="projects_file" type="select" format="json" label="MiCall-Lite Projects File"> + <options from_data_table="micall_lite_projects_files"> + <validator type="no_options" message="No MiCall-Lite projects files are available" /> + </options> + </param> + </when> + <when value="history"> + <param name="projects_file" type="data" format="json" label="MiCall-Lite Projects File" help=""/> + </when> + </conditional> <param name="readlen" type="integer" min="1" value="251" max="600" label="Read Length" help="Read Length" /> </inputs> <outputs> @@ -82,6 +110,9 @@ </outputs> <tests> <test> + <conditional name="projects_file_source" > + <param name="projects_file_source_selector" value="none" /> + </conditional> <conditional name="fastq_input"> <param name="fastq_input_selector" value="paired"/> <param name="reads1" value="1234A-V3LOOP_S1_L001_R1_001.fastq" /> @@ -95,6 +126,9 @@ <output name="nuc" value="1234A-V3LOOP.nuc.csv" /> </test> <test> + <conditional name="projects_file_source" > + <param name="projects_file_source_selector" value="none" /> + </conditional> <conditional name="fastq_input"> <param name="fastq_input_selector" value="paired"/> <param name="reads1" value="1234A-V3LOOP_S1_L001_R1_001.fastq.gz" /> @@ -108,6 +142,9 @@ <output name="nuc" value="1234A-V3LOOP.nuc.csv" /> </test> <test> + <conditional name="projects_file_source" > + <param name="projects_file_source_selector" value="none" /> + </conditional> <conditional name="fastq_input"> <param name="fastq_input_selector" value="paired_collection" /> <param name="pair" > @@ -125,6 +162,9 @@ <output name="nuc" value="1234A-V3LOOP.nuc.csv" /> </test> <test> + <conditional name="projects_file_source" > + <param name="projects_file_source_selector" value="none" /> + </conditional> <conditional name="fastq_input"> <param name="fastq_input_selector" value="paired_collection" /> <param name="pair" >