Mercurial > repos > bgruening > trim_galore

comparison trim_galore.xml @ 7:8352713cf939 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 07148c518916e16602ea26473d00358fe04bc3b6-dirty
author bgruening
date Mon, 25 Jan 2016 04:44:33 -0500
parents 11962ce40855
children f1e71aeaa923
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6:11962ce40855 7:8352713cf939
1 <tool id="trim_galore" name="Trim Galore!" version="0.4.0"> 1 <tool id="trim_galore" name="Trim Galore!" version="0.4.1">
2 <!-- Wrapper compatible with Trim Galore! version 0.4 --> 2 <!-- Wrapper compatible with Trim Galore! version 0.4 -->
3 <description>adaptive quality and adapter trimmer</description> 3 <description>adaptive quality and adapter trimmer</description>
4 <macros> 4 <macros>
5 <macro name="adapter_trimming"> 5 <macro name="adapter_trimming">
6 <conditional name="trimming"> 6 <conditional name="trimming">
9 <option value="--illumina">Illumina universal</option> 9 <option value="--illumina">Illumina universal</option>
10 <option value="--nextera">Nextera transposase</option> 10 <option value="--nextera">Nextera transposase</option>
11 <option value="--small_rna">Illumina small RNA adapters</option> 11 <option value="--small_rna">Illumina small RNA adapters</option>
12 <option value="user">User defined adapter trimming</option> 12 <option value="user">User defined adapter trimming</option>
13 </param> 13 </param>
14 <when value="auto"/> 14 <when value=""/>
15 <when value="--illumina"/> 15 <when value="--illumina"/>
16 <when value="--nextera"/> 16 <when value="--nextera"/>
17 <when value="--small_rna"/> 17 <when value="--small_rna"/>
18 <when value="user"> 18 <when value="user">
19 <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed off"> 19 <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed off">
267 <data format="fastqsanger" name="trimmed_reads_pair2" from_work_dir="input_mate2_val_2.fq" 267 <data format="fastqsanger" name="trimmed_reads_pair2" from_work_dir="input_mate2_val_2.fq"
268 label="${tool.name} on ${on_string}: trimmed reads pair 2"> 268 label="${tool.name} on ${on_string}: trimmed reads pair 2">
269 <filter>singlePaired['sPaired'] == "paired"</filter> 269 <filter>singlePaired['sPaired'] == "paired"</filter>
270 </data> 270 </data>
271 271
272 <data format="fastqsanger" name="unpaired_reads_1" from_work_dir="input_mate1_val_1.fq" 272 <data format="fastqsanger" name="unpaired_reads_1" from_work_dir="input_mate1_unpaired_1.fq"
273 label="${tool.name} on ${on_string}: unpaired reads (1)"> 273 label="${tool.name} on ${on_string}: unpaired reads (1)">
274 <filter>params['settingsType'] == "custom"</filter> 274 <filter>params['settingsType'] == "custom"</filter>
275 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter> 275 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
276 <filter>singlePaired['sPaired'] == "paired"</filter> 276 <filter>singlePaired['sPaired'] == "paired"</filter>
277 </data> 277 </data>
278 278
279 <data format="fastqsanger" name="unpaired_reads_2" from_work_dir="input_mate2_val_2.fq" 279 <data format="fastqsanger" name="unpaired_reads_2" from_work_dir="input_mate2_unpaired_2.fq"
280 label="${tool.name} on ${on_string}: unpaired reads (2)"> 280 label="${tool.name} on ${on_string}: unpaired reads (2)">
281 <filter>params['settingsType'] == "custom"</filter> 281 <filter>params['settingsType'] == "custom"</filter>
282 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter> 282 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
283 <filter>singlePaired['sPaired'] == "paired"</filter> 283 <filter>singlePaired['sPaired'] == "paired"</filter>
284 </data> 284 </data>