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comparison cutadapt.xml @ 30:c5e2e5902201 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c75b6fda89f1cb0dce226ec983adda7f051a42e8"
author iuc
date Wed, 02 Mar 2022 08:37:02 +0000
parents 48f587c13075
children 5915ea1ec9b1
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29:48f587c13075 30:c5e2e5902201
2 <description>Remove adapter sequences from FASTQ/FASTA</description> 2 <description>Remove adapter sequences from FASTQ/FASTA</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro='edam_ontology' /> 6 <expand macro='edam_ontology' />
7 <expand macro='xrefs'/>
7 <expand macro='requirements' /> 8 <expand macro='requirements' />
8 <expand macro='xrefs'/>
9 <version_command>cutadapt --version</version_command> 9 <version_command>cutadapt --version</version_command>
10 10
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 ## Link in the input and output files, so Cutadapt can tell their type 12 ## Link in the input and output files, so Cutadapt can tell their type
13 13
532 </conditional> 532 </conditional>
533 </repeat> 533 </repeat>
534 </section> 534 </section>
535 <param name="output_selector" value="rest_file,json_stats"/> 535 <param name="output_selector" value="rest_file,json_stats"/>
536 <output name="out1" file="cutadapt_rest.out" ftype="fasta"/> 536 <output name="out1" file="cutadapt_rest.out" ftype="fasta"/>
537 <output name="json_stats" file="cutadapt_rest.json" ftype="json"/> 537 <output name="json_stats" file="cutadapt_rest.json" ftype="json" lines_diff="4"/> <!--allow for differing cutadapt and python version-->
538 <output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/> 538 <output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/>
539 </test> 539 </test>
540 <!-- Ensure nextseq-trim option works --> 540 <!-- Ensure nextseq-trim option works -->
541 <test expect_num_outputs="1"> 541 <test expect_num_outputs="1">
542 <param name="type" value="single" /> 542 <param name="type" value="single" />
1331 1331
1332 * {header} – the full, unchanged header 1332 * {header} – the full, unchanged header
1333 * {id} – the read ID, that is, the part of the header before the first whitespace 1333 * {id} – the read ID, that is, the part of the header before the first whitespace
1334 * {comment} – the part of the header after the whitespace following the ID 1334 * {comment} – the part of the header after the whitespace following the ID
1335 * {adapter_name} – the name of adapter that was found in this read or no_adapter if there was none adapter match. If you use --times to do multiple rounds of adapter matching, this is the name of the last found adapter. 1335 * {adapter_name} – the name of adapter that was found in this read or no_adapter if there was none adapter match. If you use --times to do multiple rounds of adapter matching, this is the name of the last found adapter.
1336 * {match_sequence} – the sequence of the read that matched the adapter (including errors). If there was no adapter match, this is set to an empty string. If you use a linked adapter, this is to the two matching strings, separated by a comma.
1336 * {cut_prefix} – the prefix removed by the --cut (or -u) option (that is, when used with a positive length argument) 1337 * {cut_prefix} – the prefix removed by the --cut (or -u) option (that is, when used with a positive length argument)
1337 * {cut_suffix} – the suffix removed by the --cut (or -u) option (that is, when used with a negative length argument) 1338 * {cut_suffix} – the suffix removed by the --cut (or -u) option (that is, when used with a negative length argument)
1339 * {rc} – this is replaced with the string rc if the read was reverse complemented. This only applies when reverse complementing was requested
1338 1340
1339 If the --rename option is used with paired-end data, the template is applied separately to both R1 and R2. That is, for R1, the placeholders are replaced with values from R1, and for R2, the placeholders are replaced with values from R2. For example, {comment} becomes R1’s comment in R1 and it becomes R2’s comment in R2. 1341 If the --rename option is used with paired-end data, the template is applied separately to both R1 and R2. That is, for R1, the placeholders are replaced with values from R1, and for R2, the placeholders are replaced with values from R2. For example, {comment} becomes R1’s comment in R1 and it becomes R2’s comment in R2.
1340 1342
1343 For paired-end data, the placeholder {rn} is available (“read number”), and it is replaced with 1 in R1 and with 2 in R2.
1344
1345 In addition, it is possible to write a placeholder as {r1.placeholdername} or {r2.placeholdername}, which always takes the replacement value from R1 or R2, respectively.
1346 The {r1.placeholder} and {r2.placeholder} notation is available for all placeholders except {rn} and {id} because the read ID needs to be identical for both reads.
1341 1347
1342 -------------------- 1348 --------------------
1343 1349
1344 **More Information** 1350 **More Information**
1345 1351