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comparison presto_collapseseq.xml @ 0:d1a1b738c119 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
author iuc
date Wed, 30 May 2018 15:36:25 -0400
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-1:000000000000 0:d1a1b738c119
1 <tool id="presto_collapseseq" name="pRESTO CollapseSeq" version="@PRESTO_VERSION@">
2 <description>Remove/collapse duplicate sequences</description>
3
4 <macros>
5 <import>presto_macros.xml</import>
6 </macros>
7
8 <expand macro="requirements"/>
9
10 <version_command>CollapseSeq.py --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[
12 ln -s '$fastq_in' in.fastq &&
13 CollapseSeq.py
14 -s in.fastq
15 -n '$n'
16 --uf $uf
17 --cf $cf
18 --act $act
19 $inner
20 $keepmiss
21
22 #if $representative.select_by == "by_min"
23 --minf '$minf'
24 #end if
25 #if $representative.select_by == "by_max"
26 --maxf '$maxf'
27 #end if
28
29 --outname=tmp
30 #if $capture_log
31 --log '$log_out'
32 #end if
33 ]]></command>
34
35 <inputs>
36 <param argument="-s" name="fastq_in" type="data" format="fastq"
37 label="Input FASTQ file" help="FASTQ file of sequences."/>
38 <param argument="-n" type="integer" value="0" label="Max Missing"
39 help="Maximum number of missing nucleotides to consider for collapsing sequences. A sequence will be considered undetermined if it contains too many missing nucleotides."/>
40 <param argument="--uf" type="text" value="" label="Unique Field(s)" help="Space-separated list of fields to match reads by."/>
41 <param argument="--cf" type="text" value="" label="Copy Field(s)" help="Space-separated list of fields to copy into the target sequence headers.">
42 <expand macro="text-regex-validator"/>
43 </param>
44 <param argument="--act" type="text" value="" label="Action(s)" help="Space-separated list of actions to take on Copy Field(s).">
45 <expand macro="text-regex-validator"/>
46 </param>
47 <param argument="--inner" type="boolean" value="false" truevalue="--inner" falsevalue="" label="Inner" help="If true, trim off any missing/undetermined bases from the ends of reads after collapsing."/>
48 <param argument="--keepmiss" type="boolean" value="false" truevalue="--keepmiss" falsevalue="" label="Keep Missing"
49 help="If specified, sequences with more missing characters than the threshold set by the -n parameter will be written to the unique sequence output file with a DUPCOUNT=1 annotation. If not specified, such sequences will be written to a separate file."/>
50 <conditional name="representative">
51 <param name="select_by" type="select">
52 <option value="first">First Sequence</option>
53 <option value="by_min">By field minimum value</option>
54 <option value="by_max">By field maximum value</option>
55 </param>
56 <when value="first"></when>
57 <when value="by_min">
58 <param argument="--minf" type="text" value="" label="Field Name" help="Specifies the field whose minimum value determines the retained sequence."/>
59 </when>
60 <when value="by_max">
61 <param argument="--maxf" type="text" value="" label="Field Name" help="Specifies the field whose maximum value determines the retained sequence."/>
62 </when>
63 </conditional>
64 <expand macro="presto-log-param"/>
65 </inputs>
66
67 <outputs>
68 <data name="fastq_out" format="fastq" from_work_dir="tmp_collapse-unique.fastq"/>
69 <expand macro="presto-log-output"/>
70 </outputs>
71
72 <tests>
73 <test>
74 <param name="fastq_in" value="presto_collapseseq_test_in.fastq"/>
75 <param name="n" value="0"/>
76 <param name="uf" value="PRCONS CREGION"/>
77 <param name="cf" value="CONSCOUNT"/>
78 <param name="act" value="sum"/>
79 <param name="inner" value="true"/>
80 <param name="keepmiss" value="true"/>
81 <output name="fastq_out" file="presto_collapseseq_test_output.fastq" sort="true"/>
82 </test>
83 </tests>
84
85 <help><![CDATA[
86 Removes/collapses duplicate sequences from FASTQ files.
87
88 See the `pRESTO online help <@PRESTO_URL_BASE@/CollapseSeq.html>`_ for more information.
89
90 @HELP_NOTE@
91 ]]></help>
92 <expand macro="citations" />
93 </tool>