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comparison tools/blast_plus_remote_blastp.xml @ 4:a51980bc0ffe

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Add the -show_gis option (NCBI-gis on the NCBI Blast website)
author Jim Johnson <jj@umn.edu>
date Mon, 04 May 2015 09:58:57 -0500
parents 9f369b905447
children
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3:9f369b905447 4:a51980bc0ffe
1 <tool id="blast_plus_remote_blastp" name="NCBI BLAST+ remote blastp" version="1.0"> 1 <tool id="blast_plus_remote_blastp" name="NCBI BLAST+ remote blastp" version="1.0.1">
2 <description>Search protein database with protein query sequence(s)</description> 2 <description>Search protein database with protein query sequence(s)</description>
3 <parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism> 3 <parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism>
4 <version_command>blastp -version</version_command> 4 <version_command>blastp -version</version_command>
5 <requirements> 5 <requirements>
6 <requirement type="binary">blastp</requirement> 6 <requirement type="binary">blastp</requirement>
41 -task $blast_type 41 -task $blast_type
42 -evalue $evalue_cutoff 42 -evalue $evalue_cutoff
43 -out blast_output 43 -out blast_output
44 ##Set the extended list here so if/when we add things, saved workflows are not affected 44 ##Set the extended list here so if/when we add things, saved workflows are not affected
45 #if str($fmt_opt.out_format)=="text": 45 #if str($fmt_opt.out_format)=="text":
46 -outfmt "$fmt_opt.outfmt" $fmt_opt.html 46 -outfmt "$fmt_opt.outfmt" $fmt_opt.html $fmt_opt.show_gis
47 #if $fmt_opt.num_descriptions.__str__.strip() != '': 47 #if $fmt_opt.num_descriptions.__str__.strip() != '':
48 -num_descriptions $fmt_opt.num_descriptions 48 -num_descriptions $fmt_opt.num_descriptions
49 #end if 49 #end if
50 #if $fmt_opt.num_alignments.__str__.strip() != '': 50 #if $fmt_opt.num_alignments.__str__.strip() != '':
51 -num_alignments $fmt_opt.num_alignments 51 -num_alignments $fmt_opt.num_alignments
160 <option value="2">Query-anchored text</option> 160 <option value="2">Query-anchored text</option>
161 <option value="3">Flat query-anchored text showing identitites</option> 161 <option value="3">Flat query-anchored text showing identitites</option>
162 <option value="4">Flat query-anchored text</option> 162 <option value="4">Flat query-anchored text</option>
163 </param> 163 </param>
164 <param name="html" type="boolean" label="Html" truevalue="-html" falsevalue="" checked="true" /> 164 <param name="html" type="boolean" label="Html" truevalue="-html" falsevalue="" checked="true" />
165 <param name="show_gis" type="boolean" label="NCBI-gis" truevalue="-show_gis" falsevalue="" checked="false"
166 help="Show the NCBI gis in the Subject def lines"/>
165 <param name="num_descriptions" type="integer" value="500" optional="true" label="Maximum Decriptions to show" help="Show one-line descriptions for this number of database sequences."> 167 <param name="num_descriptions" type="integer" value="500" optional="true" label="Maximum Decriptions to show" help="Show one-line descriptions for this number of database sequences.">
166 <validator type="in_range" min="0" /> 168 <validator type="in_range" min="0" />
167 </param> 169 </param>
168 <param name="num_alignments" type="integer" value="250" optional="true" label="Maximum alignments to show" help="Show alignments for this number of database sequences."> 170 <param name="num_alignments" type="integer" value="250" optional="true" label="Maximum alignments to show" help="Show alignments for this number of database sequences.">
169 <validator type="in_range" min="0" /> 171 <validator type="in_range" min="0" />