Mercurial > repos > greg > gene_family_classifier
changeset 20:038777896b71 draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 10 Jan 2017 10:16:18 -0500 |
| parents | c4a9c23334a4 |
| children | 795745116516 |
| files | gene_family_classifier.xml |
| diffstat | 1 files changed, 7 insertions(+), 1 deletions(-) [+] |
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--- 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 + ]]> </command> <inputs>