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comparison sortmerna.xml @ 4:5d7ec21f6d4c draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 4d9df680f128bc18183ebba6f85fc24f11207571-dirty
author bebatut
date Wed, 28 Oct 2015 08:29:15 -0400
parents 9c19086ae626
children 064dbe9f9333
comparison
equal deleted inserted replaced
3:9c19086ae626 4:5d7ec21f6d4c
49 --other other_file 49 --other other_file
50 #end if 50 #end if
51 #end if 51 #end if
52 52
53 #if $sam.test: 53 #if $sam.test:
54 --aligned $sam_alignment_file
55 --sam 54 --sam
56 $sam.sq_tag 55 $sam.sq_tag
57 #end if 56 #end if
58 57
59 #if $blast.test: 58 #if $blast.test:
60 --aligned $blast_output_file
61 --blast "$blast.format" 59 --blast "$blast.format"
62 #end if 60 #end if
63 61
64 $log.test 62 $log
65 63
66 #if $report.type == 'best': 64 #if $report.type == 'best':
67 #if $report.best.type == '0': 65 #if $report.best.type == '0':
68 --best 0 66 --best 0
69 #else if $report.best.type == '1': 67 #else if $report.best.type == '1':
144 <option value="1 cigar qcov qstrand">Tabular + columns for CIGAR, query coverage and strand</option> 142 <option value="1 cigar qcov qstrand">Tabular + columns for CIGAR, query coverage and strand</option>
145 </param> 143 </param>
146 </when> 144 </when>
147 </conditional> 145 </conditional>
148 146
149 <conditional name="log"> 147 <param name='log' type='boolean' checked="true" truevalue='--log' falsevalue='' label="Conserve overall statistic output into a log file?" help=""/>
150 <param name='test' type='boolean' checked="true" truevalue='--log' falsevalue='' label="Conserve overall statistic output into a log file?" help=""/>
151 </conditional>
152 148
153 <conditional name="report"> 149 <conditional name="report">
154 <param name="type" type="select" display="radio" label="Parameters for filtering and read mapping" help=""> 150 <param name="type" type="select" display="radio" label="Parameters for filtering and read mapping" help="">
155 <option value="best" selected="true">Report best alignments per read reaching E-value</option> 151 <option value="best" selected="true">Report best alignments per read reaching E-value</option>
156 <option value="num_alignments">Report first alignements per read reaching E-value</option> 152 <option value="num_alignments">Report first alignements per read reaching E-value</option>
221 <when input="blast.format" value="0" format="txt" /> 217 <when input="blast.format" value="0" format="txt" />
222 </change_format> 218 </change_format>
223 </data> 219 </data>
224 220
225 <data format="txt" name="output_log" metadata="input_sequence_file" from_work_dir="aligned.log"> 221 <data format="txt" name="output_log" metadata="input_sequence_file" from_work_dir="aligned.log">
226 <filter>log.test</filter> 222 <filter>log</filter>
227 </data> 223 </data>
228 </outputs> 224 </outputs>
229 225
230 <tests> 226 <tests>
231 <test> 227 <test>