Mercurial > repos > greg > gene_family_classifier
changeset 39:c4f809cd2f38 draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 06 Feb 2017 09:04:44 -0500 |
| parents | b63f96ff6708 |
| children | 6cf0fff77dea |
| files | gene_family_classifier.xml |
| diffstat | 1 files changed, 16 insertions(+), 14 deletions(-) [+] |
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--- a/gene_family_classifier.xml Thu Feb 02 14:41:34 2017 -0500 +++ b/gene_family_classifier.xml Mon Feb 06 09:04:44 2017 -0500 @@ -13,10 +13,10 @@ </stdio> <command> <![CDATA[ - #import os - #set scaffold_path = $scaffold.fields.path - #set scaffold_dir = $os.path.split($scaffold_path)[0] - #set scaffold_selection = $os.path.split($scaffold_path)[1] + #import os + #set scaffold_path = $scaffold.fields.path + #set scaffold_dir = $os.path.split($scaffold_path)[0] + #set scaffold_selection = $os.path.split($scaffold_path)[1] #if str($options_type.options_type_selector) == 'advanced': #set create_orthogroup_cond = $options_type.create_orthogroup_cond @@ -33,10 +33,10 @@ #set create_ortho_sequences = True #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta') #if $create_corresponding_coding_sequences: - #set dest_dir = $output_ptcgfcs.extra_files_path + #set dest_dir = $output_ptcgfcs.extra_files_path #else: - #set dest_dir = $output_ptcgf.extra_files_path - #end if + #set dest_dir = $output_ptcgf.extra_files_path + #end if mkdir -p $dest_dir && #else: #set create_ortho_sequences = False @@ -79,11 +79,13 @@ #if $create_ortho_sequences: #if $create_corresponding_coding_sequences: - && echo "# Precomputed orthologous gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_ptcgfcs - && ls -al $orthogroups_fasta_src_dir | grep f >> $output_ptcgfcs + && echo '#Precomputed orthologous gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files' > $output_ptcgfcs + && echo '#Size File' > $output_ptcgfcs + && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptcgfcs #else: - && echo "# Precomputed orthologous gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_ptcgf - && ls -al $orthogroups_fasta_src_dir | grep f >> $output_ptcgf + && echo '#Precomputed orthologous gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files' > $output_ptcgf + && echo '#Size File' > $output_ptcgf + && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptcgf #end if && mv $orthogroups_fasta_src_dir/* $dest_dir || true #end if @@ -94,7 +96,7 @@ <param name="input" format="fasta" type="data" label="Amino acids (proteins) sequences fasta file"/> <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> <options from_data_table="plant_tribes_scaffolds" /> - <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool to install and populate the PlantTribes scaffolds data table."/> + <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table."/> </param> <param name="method" type="select" label="Protein clustering method"> <option value="gfam" selected="true">GFam</option> @@ -180,8 +182,8 @@ </collection> </outputs> <tests> - <!-- Not sure how to test this since the tool requires scaffolds data which is extremely large and installed using a Data Manager --> - <!-- + <!-- Not sure how to test this since the tool requires scaffolds data which is extremely large and installed using a Data Manager --> + <!-- <test> <param name="input" value="transcripts.cleaned.nr.pep" ftype="fasta" /> <param name="scaffold" value="22Gv1.1"/>