Mercurial > repos > iuc > fastp
comparison macros.xml @ 11:c59d48774d03 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
author | iuc |
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date | Tue, 05 Mar 2024 08:41:43 +0000 |
parents | 65b93b623c77 |
children | d60c3f704da0 |
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10:65b93b623c77 | 11:c59d48774d03 |
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1 <macros> | 1 <macros> |
2 <token name="@WRAPPER_VERSION@">0.23.2</token> | 2 <token name="@TOOL_VERSION@">0.23.4</token> |
3 | 3 <xml name="biotools"> |
4 <xrefs> | |
5 <xref type="bio.tools"> | |
6 fastp | |
7 </xref> | |
8 </xrefs> | |
9 </xml> | |
4 <xml name="adapter_trimming_options"> | 10 <xml name="adapter_trimming_options"> |
5 <section name="adapter_trimming_options" title="Adapter Trimming Options" expanded="False"> | 11 <section name="adapter_trimming_options" title="Adapter Trimming Options" expanded="False"> |
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."/> | 12 <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."/> |
7 <expand macro="adapter_sequence" read_number="1" /> | 13 <expand macro="adapter_sequence" read_number="1" /> |
8 <yield /> | 14 <yield /> |
9 </section> | |
10 <section name="global_trimming_options" title="Global Trimming Options" expanded="False"> | |
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."/> | |
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."/> | |
13 </section> | 15 </section> |
14 </xml> | 16 </xml> |
15 | 17 |
16 <xml name="global_trimming_options"> | 18 <xml name="global_trimming_options"> |
17 <section name="global_trimming_options" title="Global trimming options" expanded="False"> | 19 <section name="global_trimming_options" title="Global trimming options" expanded="False"> |
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."/> | 29 <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."/> |
28 </expand> | 30 </expand> |
29 </xml> | 31 </xml> |
30 | 32 |
31 <xml name="adapter_sequence" token_read_number="1"> | 33 <xml name="adapter_sequence" token_read_number="1"> |
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."> | 34 <param 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."> |
33 <sanitizer> | 35 <sanitizer> |
34 <valid> | 36 <valid> |
35 <add value="A"/> | 37 <add value="A"/> |
36 <add value="T"/> | 38 <add value="T"/> |
37 <add value="C"/> | 39 <add value="C"/> |
44 <xml name="in" token_read_number="1" token_argument="-i"> | 46 <xml name="in" token_read_number="1" token_argument="-i"> |
45 <param name="in@READ_NUMBER@" argument="@ARGUMENT@" type="data" format="fastq,fastq.gz" label="Input @READ_NUMBER@" help="Input FASTQ file #@READ_NUMBER@"/> | 47 <param name="in@READ_NUMBER@" argument="@ARGUMENT@" type="data" format="fastq,fastq.gz" label="Input @READ_NUMBER@" help="Input FASTQ file #@READ_NUMBER@"/> |
46 </xml> | 48 </xml> |
47 | 49 |
48 <xml name="poly_g_min_len"> | 50 <xml name="poly_g_min_len"> |
49 <param name="poly_g_min_len" argument="--poly_g_min_len" type="integer" optional="true" label="PolyG minimum length" | 51 <param argument="--poly_g_min_len" type="integer" optional="true" label="PolyG minimum length" |
50 help="The minimum length to detect polyG in the read tail. 10 by default."/> | 52 help="The minimum length to detect polyG in the read tail. 10 by default."/> |
51 </xml> | 53 </xml> |
52 </macros> | 54 </macros> |