Mercurial > repos > greg > gene_family_classifier
changeset 15:9d4ec1102803 draft
Uploaded
| author | greg |
|---|---|
| date | Wed, 04 Jan 2017 14:51:30 -0500 |
| parents | 595088cc480a |
| children | 1cf39b1af248 |
| files | gene_family_classifier.xml |
| diffstat | 1 files changed, 8 insertions(+), 8 deletions(-) [+] |
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--- a/gene_family_classifier.xml Wed Jan 04 14:30:12 2017 -0500 +++ b/gene_family_classifier.xml Wed Jan 04 14:51:30 2017 -0500 @@ -15,7 +15,7 @@ #if str($options_type.options_type_selector) == 'advanced' and str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes': #import os #set create_ortho_sequences = True - #set src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta') + #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta') #set dest_dir = $output.extra_files_path mkdir -p $dest_dir && #else: @@ -41,14 +41,14 @@ --num_threads \${GALAXY_SLOTS:-4} #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both': #if str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes': - && mv $src_dir/hmmscan.log $hmmscan_log + && mv geneFamilyClassification_dir/hmmscan.log $hmmscan_log #else: - && rm $src_dir/hmmscan.log + && rm geneFamilyClassification_dir/hmmscan.log #end if #end if #if $create_ortho_sequences: - && echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $src_dir | wc -l` files" > $output - && mv $src_dir/* $dest_dir + && echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $orthogroups_fasta_src_dir | wc -l` files" > $output + && mv $orthogroups_fasta_src_dir/* $dest_dir #end if ]]> </command> @@ -119,12 +119,12 @@ </conditional> </inputs> <outputs> + <data name="hmmscan_log" format="txt" label="Protein classification hmmscan.log on ${on_string}"> + <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter> + </data> <data name="output" format="txt" label="Sequences classified into gene family clusters on ${on_string}"> <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes'</filter> </data> - <data name="hmmscan_log" format="txt" label="Protein classification hmmscan.log on ${on_string}"> - <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter> - </data> <collection name="transcripts" type="list"> <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" /> </collection>