Mercurial > repos > bgruening > repeat_masker

comparison repeatmasker.xml @ 6:65ab76d58c41 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 6cf009024dfff81b0e0f836b76cf475e7cf84c71
author iuc
date Tue, 18 Dec 2018 14:05:17 -0500
parents 8404aa79a631
children d7540a923c7b
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5:8404aa79a631 6:65ab76d58c41
1 <tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.7+galaxy1" profile="17.01"> 1 <tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.7+galaxy2" profile="17.01">
2 <description>RepeatMasker</description> 2 <description>RepeatMasker</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="4.0.7">repeatmasker</requirement> 5 <requirement type="package" version="4.0.7">repeatmasker</requirement>
6 </requirements> 6 </requirements>
7 7
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 RM_LIB_PATH=\$(dirname \$(which RepeatMasker))/../share/RepeatMasker/Libraries && 9 RM_PATH=\$(which RepeatMasker) &&
10 if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi &&
11 RM_LIB_PATH=\$(dirname \$RM_PATH)/../share/RepeatMasker/Libraries &&
10 mkdir lib && 12 mkdir lib &&
11 export REPEATMASKER_LIB_DIR=\$(pwd)/lib && 13 export REPEATMASKER_LIB_DIR=\$(pwd)/lib &&
12 for file in \$(ls \$RM_LIB_PATH) ; do ln -s \$RM_LIB_PATH/\$file lib/\$file ; done && 14 for file in \$(ls \$RM_LIB_PATH) ; do ln -s \$RM_LIB_PATH/\$file lib/\$file ; done &&
13 #if $repeat_source.source_type == "repbase": 15 #if $repeat_source.source_type == "repbase":
14 cp '${repeat_source.repbase_file}' 'lib/${repeat_source.repbase_file_name}' && 16 cp '${repeat_source.repbase_file}' 'lib/${repeat_source.repbase_file_name}' &&
187 <test expect_num_outputs="4"> 189 <test expect_num_outputs="4">
188 <param name="input_fasta" value="small.fasta" ftype="fasta" /> 190 <param name="input_fasta" value="small.fasta" ftype="fasta" />
189 <param name="source_type" value="library" /> 191 <param name="source_type" value="library" />
190 <param name="repeat_lib" value="repeats.fasta" ftype="fasta" /> 192 <param name="repeat_lib" value="repeats.fasta" ftype="fasta" />
191 <output name="output_masked_genome" file="small.fasta.masked" /> 193 <output name="output_masked_genome" file="small.fasta.masked" />
192 <output name="output_table" file="small.fasta.stats" lines_diff="2" /> 194 <output name="output_table" file="small.fasta.stats" lines_diff="4" />
193 <output name="output_repeat_catalog" file="small.fasta.cat" /> 195 <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" />
194 <output name="output_log" file="small.fasta.log" /> 196 <output name="output_log" file="small.fasta.log" />
195 </test> 197 </test>
196 <test expect_num_outputs="7"> 198 <test expect_num_outputs="7">
197 <param name="input_fasta" value="small.fasta" ftype="fasta" /> 199 <param name="input_fasta" value="small.fasta" ftype="fasta" />
198 <param name="source_type" value="library" /> 200 <param name="source_type" value="library" />
200 <!-- <param name="show" value="yes" /> --> 202 <!-- <param name="show" value="yes" /> -->
201 <param name="keep_alignments" value="-ali" /> 203 <param name="keep_alignments" value="-ali" />
202 <param name="poly" value="-poly" /> 204 <param name="poly" value="-poly" />
203 <param name="repeat_lib" value="repeats.fasta" ftype="fasta" /> 205 <param name="repeat_lib" value="repeats.fasta" ftype="fasta" />
204 <output name="output_masked_genome" file="small.fasta.masked" /> 206 <output name="output_masked_genome" file="small.fasta.masked" />
205 <output name="output_table" file="small.fasta.stats" lines_diff="4" /> 207 <output name="output_table" file="small.fasta.stats" lines_diff="6" />
206 <output name="output_repeat_catalog" file="small.fasta.cat" /> 208 <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" />
207 <output name="output_log" file="small.fasta.log" /> 209 <output name="output_log" file="small.fasta.log" />
208 <output name="output_alignment" file="small.fasta.align" /> 210 <output name="output_alignment" file="small.fasta.align" />
209 <output name="output_polymorphic" file="small.fasta.poly" /> 211 <output name="output_polymorphic" file="small.fasta.poly" />
210 <output name="output_gff" file="small.fasta.gff" lines_diff="4" /> 212 <output name="output_gff" file="small.fasta.gff" lines_diff="4" />
211 </test> 213 </test>
215 <param name="repbase_file" value="fake_repbase.embl" /> 217 <param name="repbase_file" value="fake_repbase.embl" />
216 <param name="repbase_file_name" value="fake.embl" /> 218 <param name="repbase_file_name" value="fake.embl" />
217 <param name="species_list" value="anopheles" /> 219 <param name="species_list" value="anopheles" />
218 <output name="output_masked_genome" file="small.fasta.masked" /> 220 <output name="output_masked_genome" file="small.fasta.masked" />
219 <output name="output_table" file="small_repbase.fasta.stats" lines_diff="2" /> 221 <output name="output_table" file="small_repbase.fasta.stats" lines_diff="2" />
220 <output name="output_repeat_catalog" file="small.fasta.cat" /> 222 <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" />
221 <output name="output_log" file="small_repbase.fasta.log" /> 223 <output name="output_log" file="small_repbase.fasta.log" />
222 </test> 224 </test>
223 </tests> 225 </tests>
224 <help><![CDATA[ 226 <help><![CDATA[
225 RepeatMasker is a program that screens DNA for interspersed repeats and low 227 RepeatMasker is a program that screens DNA for interspersed repeats and low