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comparison sortmerna.xml @ 6:97f73e0566c9 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
author rnateam
date Tue, 29 Mar 2016 06:53:28 -0400
parents 233da82dc31c
children bf2866308fbd
comparison
equal deleted inserted replaced
5:233da82dc31c 6:97f73e0566c9
1 <tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.1.0"> 1 <tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.1b.0">
2 <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description> 2 <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description>
3 <requirements> 3 <requirements>
4 <requirement type='package' version="2.0">sortmerna</requirement> 4 <requirement type="package" version="2.1b">sortmerna</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <regex match="This program builds a Burst trie on an input rRNA database" 7 <regex match="This program builds a Burst trie on an input rRNA database"
8 source="both" 8 source="both"
9 level="fatal" 9 level="fatal"
10 description="Buildtrie program failed to execute." /> 10 description="Buildtrie program failed to execute." />
11 <regex match="The database name" 11 <regex match="The database name"
12 source="both" 12 source="both"
13 level="fatal" 13 level="fatal"
14 description="The database ${databases} has not been preprocessed using buildtrie before using SortMeRNA." /> 14 description="The database ${databases} has not been preprocessed using buildtrie before using SortMeRNA." />
15 <regex match="ERROR"
16 source="both"
17 level="fatal"
18 description="ERROR" />
15 </stdio> 19 </stdio>
16 <version_command> 20 <version_command>
17 <![CDATA[ 21 <![CDATA[
18 sortmerna --version 2>&1|grep 'SortMeRNA version' 22 sortmerna --version 2>&1|grep 'SortMeRNA version'
19 ]]> 23 ]]>
74 $aligned_blast 78 $aligned_blast
75 79
76 $log 80 $log
77 81
78 #if $report.report_type == 'best' 82 #if $report.report_type == 'best'
79 #if $report.report_best.report_best_type == '0' 83 #if $report.report_best.report_best_type == '1'
80 --best 0
81 #else if $report.report_best.report_best_type == '1'
82 --best 1 84 --best 1
83 --min_lis $report.report_best.report_best_min_lis 85 --min_lis $report.report_best.report_best_min_lis
84 #else 86 #else
85 --best $report.report_best.report_best_value 87 --best $report.report_best.report_best_value
86 --min_lis $report.report_best.report_best_min_lis 88 --min_lis $report.report_best.report_best_min_lis
193 <option value="num_alignments">Report first alignements per read reaching E-value</option> 195 <option value="num_alignments">Report first alignements per read reaching E-value</option>
194 </param> 196 </param>
195 <when value="best"> 197 <when value="best">
196 <conditional name="report_best"> 198 <conditional name="report_best">
197 <param name="report_best_type" type="select" label="Number of searched alignments" help="Only the best alignment is reported (--best)"> 199 <param name="report_best_type" type="select" label="Number of searched alignments" help="Only the best alignment is reported (--best)">
198 <option value="0">All high-candidate reference sequences are searched for alignments (very slow)</option>
199 <option value="1" selected="true">Only one high-candidate reference sequence is searched for alignments (fast). The high-candidate sequences are determined heuristically using a LIS of seed matches)</option> 200 <option value="1" selected="true">Only one high-candidate reference sequence is searched for alignments (fast). The high-candidate sequences are determined heuristically using a LIS of seed matches)</option>
200 <option value="other_value">A custom number of reference sequences are searched for alignments (speed decrease for high value)</option> 201 <option value="other_value">A custom number of reference sequences are searched for alignments (speed decrease for high value)</option>
201 </param> 202 </param>
202 <when value="0" />
203 <when value="1"> 203 <when value="1">
204 <param name="report_best_min_lis" type="integer" min="0" max="100" value="2" label="Number of longest LIS an alignement needs to be searched" help="The alignements having the first INT longest LIS. LIS stands for Longest Increasing Subsequence, it is computed using seeds' positions to expand hits into longer matches prior to Smith-Waterman alignment. (--min_lis)"/> 204 <param name="report_best_min_lis" type="integer" min="0" max="100" value="2" label="Number of longest LIS an alignement needs to be searched" help="The alignements having the first INT longest LIS. LIS stands for Longest Increasing Subsequence, it is computed using seeds' positions to expand hits into longer matches prior to Smith-Waterman alignment. (--min_lis)"/>
205 </when> 205 </when>
206 <when value="other_value"> 206 <when value="other_value">
207 <param name="report_best_value" type="integer" min="2" max="100" value="2" label="Number of alignments to be made" help="Only the best one is reported. The computation speed decrease with high value"/> 207 <param name="report_best_value" type="integer" min="2" max="100" value="2" label="Number of alignments to be made" help="Only the best one is reported. The computation speed decrease with high value"/>