Mercurial > repos > iuc > fastp

annotate macros.xml @ 7:6c2351178f8d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 249269561e1d3a767371c154677e5dd59147f7d7
author iuc
date Wed, 16 Jan 2019 04:02:33 -0500
parents 3e2551a37201
children dbf9c561ef29
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
1 <macros>
7
6c2351178f8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 249269561e1d3a767371c154677e5dd59147f7d7
iuc
parents: 5
diff changeset
2 <token name="@WRAPPER_VERSION@">0.19.5</token>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
3
5
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
4 <xml name="adapter_trimming_options">
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
5 <section name="adapter_trimming_options" title="Adapter Trimming Options" expanded="False">
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
6 <param name="disable_adapter_trimming" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Disable adapter trimming" help="Adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled."/>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
7 <expand macro="adapter_sequence" read_number="1" />
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
8 <yield />
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
9 </section>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
10 <section name="global_trimming_options" title="Global Trimming Options" expanded="False">
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
11 <param name="trim_front1" argument="-f" type="integer" optional="true" label="Trim front for input 1" help="Trimming how many bases in front for read1, default is 0."/>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
12 <param name="trim_tail1" argument="-t" type="integer" optional="true" label="Trim tail for input 1" help="Trimming how many bases in tail for read1, default is 0."/>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
13 </section>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
14 </xml>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
15
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
16 <xml name="global_trimming_options">
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
17 <section name="global_trimming_options" title="Global trimming options" expanded="False">
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
18 <param name="trim_front1" argument="-f" type="integer" optional="true" label="Trim front for input 1" help="Trimming how many bases in front for read1, default is 0."/>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
19 <param name="trim_tail1" argument="-t" type="integer" optional="true" label="Trim tail for input 1" help="Trimming how many bases in tail for read1, default is 0."/>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
20 <yield/>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
21 </section>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
22 </xml>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
23
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
24 <xml name="global_trimming_options_paired">
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
25 <expand macro="global_trimming_options">
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
26 <param name="trim_front2" argument="-F" type="integer" optional="true" label="Trim front for input 2" help="Trimming how many bases in front for read2. If it's not specified, it will follow read1's settings."/>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
27 <param name="trim_tail2" argument="-T" type="integer" optional="true" label="Trim tail for input 2" help="Trimming how many bases in tail for read2. If it's not specified, it will follow read1's settings."/>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
28 </expand>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
29 </xml>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
30
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
31 <xml name="adapter_sequence" token_read_number="1">
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
32 <param name="adapter_sequence@READ_NUMBER@" argument="--adapter_sequence@READ_NUMBER@" type="text" optional="true" label="Adapter sequence for input @READ_NUMBER@" help="The adapter for read@READ_NUMBER@. For SE data, if not specified, the adapter will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped.">
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
33 <sanitizer>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
34 <valid>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
35 <add value="A"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
36 <add value="T"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
37 <add value="C"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
38 <add value="G"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
39 </valid>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
40 </sanitizer>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
41 </param>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
42 </xml>
5
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
43
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
44 <xml name="in" token_read_number="1" token_argument="-i">
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
45 <param name="in@READ_NUMBER@" argument="@ARGUMENT@" type="data" format="fastq,fastq.gz" label="Input @READ_NUMBER@" help="Input FASTQ file #@READ_NUMBER@"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
46 </xml>
5
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 3
diff changeset
47
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
48 <xml name="poly_g_min_len">
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
49 <param name="poly_g_min_len" argument="--poly_g_min_len" type="integer" optional="true" label="PolyG minimum length"
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
50 help="The minimum length to detect polyG in the read tail. 10 by default."/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
51 </xml>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
52 </macros>