# HG changeset patch # User greg # Date 1484061378 18000 # Node ID 038777896b71fac61e70bea1ea24e62ee483c7bc # Parent c4a9c23334a499d66a726a04b76c8b6f32b2b133 Uploaded diff -r c4a9c23334a4 -r 038777896b71 gene_family_classifier.xml --- a/gene_family_classifier.xml Tue Jan 10 09:53:25 2017 -0500 +++ b/gene_family_classifier.xml Tue Jan 10 10:16:18 2017 -0500 @@ -24,16 +24,18 @@ #set create_corresponding_coding_sequences = True #else: #set create_corresponding_coding_sequences = False - #endif + #end if mkdir -p $dest_dir && #else: #set create_ortho_sequences = False #end if + GeneFamilyClassifier --proteins "$input" --scaffold "$scaffold" --method $method --classifier $save_hmmscan_log_cond.classifier + #if str($options_type.options_type_selector) == 'advanced': --super_orthogroups $options_type.super_orthogroups #if str($options_type.single_copy_cond) == 'taxa': @@ -47,8 +49,10 @@ #end if #end if #end if + --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds" --num_threads "\${GALAXY_SLOTS:-4}" + #if str($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 geneFamilyClassification_dir/hmmscan.log $hmmscan_log @@ -56,6 +60,7 @@ && rm geneFamilyClassification_dir/hmmscan.log #end if #end if + #if $create_ortho_sequences: #if $create_corresponding_coding_sequences: && echo "Sequences classified into pre-computed orthologous plant gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | wc -l` files" > $output @@ -65,6 +70,7 @@ && ls $orthogroups_fasta_src_dir >> $output && mv $orthogroups_fasta_src_dir/* $dest_dir #end if + ]]>