Mercurial > repos > galaxyp > blast_plus_remote_blastp
comparison tools/blast_plus_remote_blastp.xml @ 4:a51980bc0ffe
Add the -show_gis option (NCBI-gis on the NCBI Blast website)
author | Jim Johnson <jj@umn.edu> |
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date | Mon, 04 May 2015 09:58:57 -0500 |
parents | 9f369b905447 |
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3:9f369b905447 | 4:a51980bc0ffe |
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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" /> |