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comparison macros.xml @ 11:c59d48774d03 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
author iuc
date Tue, 05 Mar 2024 08:41:43 +0000
parents 65b93b623c77
children
comparison
equal deleted inserted replaced
10:65b93b623c77 11:c59d48774d03
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>