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comparison smalt_map.xml @ 1:fae9ec82e10f draft

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"planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
author nml
date Wed, 17 Jun 2020 09:47:13 -0400
parents 51ad86498414
children 5ba47ab90254
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0:51ad86498414 1:fae9ec82e10f
1 <tool id="smalt" name="smalt" version="1.0.0" > 1 <tool id="smalt" name="smalt" version="@VERSION@+galaxy0">
2 <description>Map query reads (FASTA/FASTQ) format onto the reference sequences</description> 2 <description>Map query reads (FASTA/FASTQ) format onto the reference sequences</description>
3 <macros>
4 <token name="@VERSION@">0.7.6</token>
5 <token name="@INPUT_TYPES@">fastq,fastq.gz,fastqsanger,fastqsanger.gz</token>
6 </macros>
3 <requirements> 7 <requirements>
4 <requirement type="package" version="0.7.6">smalt</requirement> 8 <requirement type="package" version="@VERSION@">smalt</requirement>
5 <requirement type="package" version="1.5">samtools</requirement> 9 <requirement type="package" version="1.5">samtools</requirement>
6 </requirements> 10 </requirements>
7 <stdio> 11 <stdio>
8 <exit_code range="1:" level="fatal" description="Unknown error" /> 12 <exit_code range="1:" level="fatal" description="Unknown error" />
9 <regex match="Command line error" 13 <regex match="Command line error"
130 <option value="single">Single-end</option> 134 <option value="single">Single-end</option>
131 <option value="paired">Paired-end</option> 135 <option value="paired">Paired-end</option>
132 <option value="collections">Paired-end Collections</option> 136 <option value="collections">Paired-end Collections</option>
133 </param> 137 </param>
134 <when value="single"> 138 <when value="single">
135 <param name="sInput1" type="data" format="fastq" label="Single end illumina fastq file" optional="false"/> 139 <param name="sInput1" type="data" format="@INPUT_TYPES@" label="Single end illumina fastq file" optional="false"/>
136 </when> 140 </when>
137 <when value="paired"> 141 <when value="paired">
138 <param name="pInput1" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/> 142 <param name="pInput1" type="data" format="@INPUT_TYPES@" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
139 <param name="pInput2" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"/> 143 <param name="pInput2" type="data" format="@INPUT_TYPES@" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"/>
140 <param name="pairtype" type="select" label="Pair Type" help="Type of read pair library"> 144 <param name="pairtype" type="select" label="Pair Type" help="Type of read pair library">
141 <option value="pe">Illumina paired-end (short inserts)</option> 145 <option value="pe">Illumina paired-end (short inserts)</option>
142 <option value="mp">Illumina mate-pair library (long inserts)</option> 146 <option value="mp">Illumina mate-pair library (long inserts)</option>
143 <option value="pp">Mate-pair sequenced on the same strand</option> 147 <option value="pp">Mate-pair sequenced on the same strand</option>
144 </param> 148 </param>
145 </when> 149 </when>
146 <when value="collections"> 150 <when value="collections">
147 <param name="fastq_collection" type="data_collection" label="Paired-end Fastq collection" help="" optional="false" format="txt" collection_type="paired" /> 151 <param name="fastq_collection" type="data_collection" label="Paired-end Fastq collection" help="" optional="false" format="@INPUT_TYPES@" collection_type="paired" />
148 <param name="pairtype" type="select" label="Pair Type" help="Type of read pair library"> 152 <param name="pairtype" type="select" label="Pair Type" help="Type of read pair library">
149 <option value="pe">Illumina paired-end (short inserts)</option> 153 <option value="pe">Illumina paired-end (short inserts)</option>
150 <option value="mp">Illumina mate-pair library (long inserts)</option> 154 <option value="mp">Illumina mate-pair library (long inserts)</option>
151 <option value="pp">Mate-pair sequenced on the same strand</option> 155 <option value="pp">Mate-pair sequenced on the same strand</option>
152 </param> 156 </param>
228 <assert_contents> 232 <assert_contents>
229 <has_text text="SN:NODE_1_length_1000_cov_140.620106" /> 233 <has_text text="SN:NODE_1_length_1000_cov_140.620106" />
230 </assert_contents> 234 </assert_contents>
231 </output> 235 </output>
232 </test> 236 </test>
237 <test>
238 <param name="sPaired" value="paired"/>
239 <param name="pInput1" value="ecoli_1K_1.fq.gz"/>
240 <param name="pInput2" value="ecoli_1K_2.fq.gz"/>
241 <param name="pairtype" value="pe"/>
242 <param name="source" value="history"/>
243 <param name="reference" value="contigs.fasta"/>
244 <param name="outformat" value="sam"/>
245 <output name="output">
246 <assert_contents>
247 <has_text text="SN:NODE_1_length_1000_cov_140.620106" />
248 </assert_contents>
249 </output>
250 </test>
233 </tests> 251 </tests>
234 <help> 252 <help>
235 253
236 **What it does** 254 **What it does**
237 255
245 263
246 .. class:: warningmark 264 .. class:: warningmark
247 265
248 There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy. 266 There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
249 267
250 .. __: http://www.sanger.ac.uk/resources/software/smalt/ 268 .. __: https://www.sanger.ac.uk/tool/smalt-0/
251 269
252 ------ 270 ------
253 271
254 **Input formats** 272 **Input formats**
255 273
256 SMALT accepts files in Sanger FASTQ format (galaxy type *fastqsanger*). Use the FASTQ Groomer to prepare your files. 274 SMALT accepts files in Sanger FASTQ format (galaxy type *fastqsanger* or *fastqsanger.gz*). Use the FASTQ Groomer to prepare your files.
257 275
258 ------ 276 ------
259 277
260 278
261 Please cite the website "http://www.sanger.ac.uk/resources/software/smalt/". 279 Please cite the website "https://www.sanger.ac.uk/tool/smalt-0/".
262 280
263 ------ 281 ------
264 282
265 283
266 -a Output explicit alignments along with the mapping coordinates. 284 -a Output explicit alignments along with the mapping coordinates.
365 -y &#060;minid FLT&#062; 383 -y &#060;minid FLT&#062;
366 Sets an identity threshold for a mapping to be reported (default: 0). 384 Sets an identity threshold for a mapping to be reported (default: 0).
367 &#060;minid&#062; specifies the number of exactly matching nucleotides either as 385 &#060;minid&#062; specifies the number of exactly matching nucleotides either as
368 a positive integer or as a fraction of the read length (&#060;= 1.0). 386 a positive integer or as a fraction of the read length (&#060;= 1.0).
369 </help> 387 </help>
388 <citations>
389 <citation type="bibtex">
390 @misc{smaltcitation,
391 author = {Ponstigl, Hannes},
392 year = {2010},
393 title = {smalt},
394 publisher = {Wellcome Trust Sanger Institute, Cambridge, UK},
395 journal = {Online},
396 url = {https://www.sanger.ac.uk/tool/smalt-0/}
397 }</citation>
398 </citations>
370 </tool> 399 </tool>