Mercurial > repos > galaxyp > blast_plus_remote_blastp

comparison blast_plus_remote_blastp.xml @ 6:e9975de58321 draft

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planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8fd454dc8332fff689a831b57ba50919a55c8277
author galaxyp
date Thu, 27 Jul 2017 17:22:20 -0400
parents 22a767177ac9
children edb3b709e165
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5:22a767177ac9 6:e9975de58321
3 <!-- If job splitting is enabled, break up the query file into parts --> 3 <!-- If job splitting is enabled, break up the query file into parts -->
4 <!-- 4 <!--
5 <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="500" merge_outputs="output1" /> 5 <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="500" merge_outputs="output1" />
6 --> 6 -->
7 <requirements> 7 <requirements>
8 <requirement type="binary">blastp</requirement>
9 <requirement type="package" version="2.6.0">blast</requirement> 8 <requirement type="package" version="2.6.0">blast</requirement>
10 </requirements> 9 </requirements>
11 <stdio> 10 <stdio>
12 <exit_code range="1" level="fatal" description="Bad input dataset or BLAST options" /> 11 <exit_code range="1" level="fatal" description="Bad input dataset or BLAST options" />
13 <exit_code range="2" level="fatal" description="Error in BLAST database" /> 12 <exit_code range="2" level="fatal" description="Error in BLAST database" />
73 #if $fmt_opt.max_target_seqs.__str__.strip() != '': 72 #if $fmt_opt.max_target_seqs.__str__.strip() != '':
74 -max_target_seqs $fmt_opt.max_target_seqs 73 -max_target_seqs $fmt_opt.max_target_seqs
75 #end if 74 #end if
76 #end if 75 #end if
77 #if $db_opts.db_opts_selector != "remote": 76 #if $db_opts.db_opts_selector != "remote":
78 -num_threads 8 77 -num_threads "\${GALAXY_SLOTS:-4}"
79 #end if 78 #end if
80 #if $adv_opts.adv_opts_selector=="advanced": 79 #if $adv_opts.adv_opts_selector=="advanced":
81 $adv_opts.filter_query 80 $adv_opts.filter_query
82 -matrix $adv_opts.scoring.matrix 81 -matrix $adv_opts.scoring.matrix
83 $adv_opts.scoring.gap_costs 82 $adv_opts.scoring.gap_costs