Mercurial > repos > greg > assembly_post_processor
changeset 6:bf355f832557 draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 30 Jan 2017 09:23:36 -0500 |
| parents | 31673ee3734f |
| children | 4d82da0ca014 |
| files | assembly_post_processor.xml |
| diffstat | 1 files changed, 16 insertions(+), 2 deletions(-) [+] |
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--- a/assembly_post_processor.xml Fri Jan 27 15:03:00 2017 -0500 +++ b/assembly_post_processor.xml Mon Jan 30 09:23:36 2017 -0500 @@ -6,7 +6,8 @@ <stdio> <!-- Anything other than zero is an error --> <exit_code range="1:" /> - <!-- In case the return code has not been set properly check stderr too --> + <exit_code range=":-1" /> + <!-- In case the return code has not been set propery check stderr too --> <regex match="Error:" /> <regex match="Exception:" /> </stdio> @@ -21,6 +22,7 @@ #if str($options_type.options_type_selector) == 'advanced': #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': --gene_family_search "$options_type.target_gene_family_assembly_cond.orthogroups" + --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds" --scaffold "$options_type.target_gene_family_assembly_cond.scaffold" --method "$options_type.target_gene_family_assembly_cond.method" #end if @@ -33,7 +35,6 @@ #end if --min_length $options_type.min_length #end if - --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds" --num_threads \${GALAXY_SLOTS:-4} ]]> </command> @@ -97,6 +98,18 @@ <test> <param name="input" value="assembly.fasta" ftype="fasta" /> <param name="prediction_method" value="transdecoder" /> + <param name="options_type_selector" value="basic" /> + <output_collection name="transcripts" type="list"> + <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" /> + <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" /> + <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta" /> + <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" /> + </output_collection> + </test> + <!-- + <test> + <param name="input" value="assembly.fasta" ftype="fasta" /> + <param name="prediction_method" value="transdecoder" /> <param name="options_type_selector" value="advanced" /> <param name="strand_specific" value="yes" /> <param name="dereplicate" value="yes" /> @@ -109,6 +122,7 @@ <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" /> </output_collection> </test> + --> </tests> <help> This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of