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comparison macros.xml @ 5:4c14c2f8f4fb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
author iuc
date Fri, 10 Aug 2018 19:13:50 -0400
parents 5f584c4b0f7e
children 2fcdbf78caf9
comparison
equal deleted inserted replaced
4:20c09892cfe7 5:4c14c2f8f4fb
1 <macros> 1 <macros>
2 <token name="@WRAPPER_VERSION@">0.19.3</token> 2 <token name="@WRAPPER_VERSION@">0.19.3</token>
3 3
4 <xml name="adapter_sequence1"> 4 <xml name="adapter_trimming_options">
5 <param name="adapter_sequence1" argument="--adapter_sequence" type="text" optional="true" label="Adapter sequence for input 1" 5 <section name="adapter_trimming_options" title="Adapter Trimming Options" expanded="False">
6 help="The adapter for read1. 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."> 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."/>
7 <expand macro="adapter_sequence" read_number="1" />
8 <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>
14 </xml>
15
16 <xml name="global_trimming_options">
17 <section name="global_trimming_options" title="Global trimming options" expanded="False">
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."/>
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."/>
20 <yield/>
21 </section>
22 </xml>
23
24 <xml name="global_trimming_options_paired">
25 <expand macro="global_trimming_options">
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."/>
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."/>
28 </expand>
29 </xml>
30
31 <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.">
7 <sanitizer> 33 <sanitizer>
8 <valid> 34 <valid>
9 <add value="A"/> 35 <add value="A"/>
10 <add value="T"/> 36 <add value="T"/>
11 <add value="C"/> 37 <add value="C"/>
12 <add value="G"/> 38 <add value="G"/>
13 </valid> 39 </valid>
14 </sanitizer> 40 </sanitizer>
15 </param> 41 </param>
16 </xml> 42 </xml>
17 <xml name="in1"> 43
18 <param name="in1" argument="-i" type="data" format="fastq,fastq.gz" label="Input 1" help="Input FASTQ file #1"/> 44 <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@"/>
19 </xml> 46 </xml>
47
20 <xml name="poly_g_min_len"> 48 <xml name="poly_g_min_len">
21 <param name="poly_g_min_len" argument="--poly_g_min_len" type="integer" optional="true" label="PolyG minimum length" 49 <param name="poly_g_min_len" argument="--poly_g_min_len" type="integer" optional="true" label="PolyG minimum length"
22 help="The minimum length to detect polyG in the read tail. 10 by default."/> 50 help="The minimum length to detect polyG in the read tail. 10 by default."/>
23 </xml> 51 </xml>
24 </macros> 52 </macros>