Mercurial > repos > mkh > ips5
diff interproscan5/ipsfaux.xml @ 3:74cf3f49f10c draft
Better HTML index.
author | mkh |
---|---|
date | Tue, 02 Feb 2016 12:27:19 -0500 |
parents | e2d4343d73ad |
children | 6574eb46426d |
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--- a/interproscan5/ipsfaux.xml Fri Jan 29 18:41:29 2016 -0500 +++ b/interproscan5/ipsfaux.xml Tue Feb 02 12:27:19 2016 -0500 @@ -1,4 +1,4 @@ -<tool id="ipsfaux" name="Faux Interproscan" version="1.0.0a"> +<tool id="ipsfaux" name="Faux Interproscan" version="1.0.1a"> <description>Interproscan functional predictions of ORFs (faux). Input file and computation options are ignored (other than the types of outputs). The same precomputed results are produced every time.</description> <requirements> @@ -12,8 +12,7 @@ <command> #import os - echo "output_types=$output_types"; - + echo "Start timestamp: \$(date)"; python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/fake_ips.py ## disables the precalculated lookup service, all calculation will be run locally -dp @@ -21,7 +20,6 @@ --seqtype $seqtype -f $output_types --applications $appl - --tempdir \$TEMP $pathways $goterms @@ -30,9 +28,7 @@ --output-file-base __base__ 2>&1; - #if 'tsv' in str($output_types): - mv __base__.tsv $tsv_file; - #end if + mv __base__.tsv $tsv_file; #if 'gff3' in str($output_types): mv __base__.gff3 $gff3_file; @@ -46,7 +42,11 @@ mkdir -p $html_file.files_path; #set temp_archive_file = '__base__.html.tar.gz' tar -C $html_file.files_path -xvmzf $temp_archive_file; - python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $html_file $html_file.files_path; + #if str($seqtype) == 'p' and not str($getorfed): + python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 0 $tsv_file $html_file $html_file.files_path; + #else + python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 1 $tsv_file $html_file $html_file.files_path; + #end if rm $temp_archive_file; #end if @@ -54,11 +54,15 @@ mkdir -p $svg_file.files_path; #set temp_archive_file = '__base__.svg.tar.gz' tar -C $svg_file.files_path -xvmzf $temp_archive_file; - python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $svg_file $svg_file.files_path; + #if str($seqtype) == 'p' and not str($getorfed): + python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 0 $tsv_file $svg_file $svg_file.files_path; + #else + python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 1 $tsv_file $svg_file $svg_file.files_path; + #end if rm $temp_archive_file; #end if - echo "End of ipsfaux" + echo "End timestamp: \$(date)" </command> <inputs> @@ -69,6 +73,10 @@ <option value="n">DNA / RNA</option> </param> + <param name="getorfed" type="boolean" label="DNA/RNA was externally processed by getorf?" help="Ignored for DNA inputs." + truevalue="getorfed" + falsevalue=""/> + <param name="mode" type="boolean" label="Run on cluster?" help="Check to submit job to cluster." truevalue="--mode=cluster --clusterrunid=gtdi-ips-analysis" falsevalue=""/> @@ -111,9 +119,8 @@ label="Provide additional mappings" help="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into (--iprlookup)"/> - <param name="output_types" type="select" display="checkboxes" multiple="true" label="Output formats" + <param name="output_types" type="select" display="checkboxes" multiple="true" label="Output formats (in addition to TSV)" help="Select the output formats to generate (at least one)"> - <option value="tsv" selected="true">Raw (TSV)</option> <option value="html" selected="true">HTML (Graphical)</option> <option value="svg" selected="false">SVG (Scalable Vector Graphics)</option> <option value="gff3" selected="true">GFF3</option> @@ -122,9 +129,7 @@ </inputs> <outputs> - <data format="tabular" name="tsv_file" label="Interproscan TSV on ${on_string}"> - <filter>'tsv' in output_types</filter> - </data> + <data format="tabular" name="tsv_file" label="Interproscan TSV on ${on_string}"/> <data format="html" name="html_file" label="Interproscan HTML on ${on_string}"> <filter>'html' in output_types</filter> </data>