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comparison fastx_clipper.xml @ 3:85263dc18cec draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 13:27:25 -0400
parents bdf1ce174e39
children 736b8f6ee456
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2:bdf1ce174e39 3:85263dc18cec
1 <tool id="cshl_fastx_clipper" name="Clip" version="1.0.1"> 1 <tool id="cshl_fastx_clipper" name="Clip" version="1.0.2">
2 <description>adapter sequences</description> 2 <description>adapter sequences</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <command> 6 <expand macro="requirements" />
7 <![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 zcat -f < '$input' | fastx_clipper -l $minlength -a '$clip_source.clip_sequence' -d $keepdelta -o '$output' -v $KEEP_N $DISCARD_OPTIONS 8 @CATS@ fastx_clipper
9 #if $input.ext == "fastqsanger": 9 -l $minlength
10 -Q 33 10 -a '$clip_source.clip_sequence'
11 #end if 11 -d $keepdelta
12 ]]> 12 -o '$output'
13 </command> 13 -v
14 $KEEP_N
15 $DISCARD_OPTIONS
16 @FQQUAL@
17 ]]></command>
14 18
15 <inputs> 19 <inputs>
16 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to clip" /> 20 <expand macro="fastx_input" />
17 21
18 <param name="minlength" type="integer" value="15"> 22 <param name="minlength" type="integer" value="15"
19 <label>Minimum sequence length (after clipping, sequences shorter than this length will be discarded)</label> 23 label="Minimum sequence length (after clipping, sequences shorter than this length will be discarded" />
20 </param>
21 24
22 <conditional name="clip_source"> 25 <conditional name="clip_source">
23 <param name="clip_source_list" type="select" label="Source"> 26 <param name="clip_source_list" type="select" label="Source">
24 <option value="prebuilt" selected="true">Standard (select from the list below)</option> 27 <option value="prebuilt" selected="true">Standard (select from the list below)</option>
25 <option value="user">Enter custom sequence</option> 28 <option value="user">Enter custom sequence</option>
37 </options> 40 </options>
38 </param> 41 </param>
39 </when> 42 </when>
40 </conditional> 43 </conditional>
41 44
42 <param name="keepdelta" type="integer" value="0"> 45 <param name="keepdelta" type="integer" value="0"
43 <label>enter non-zero value to keep the adapter sequence and x bases that follow it</label> 46 label="Enter a non-zero value to keep the adapter sequence and x bases that follow it"
44 <help>use this for hairpin barcoding. keep at 0 unless you know what you're doing.</help> 47 help="Use this for hairpin barcoding. keep at 0 unless you know what you're doing" />
45 </param>
46 48
47 <param name="KEEP_N" type="select" label="Discard sequences with unknown (N) bases"> 49 <param name="KEEP_N" type="select" label="Discard sequences with unknown (N) bases">
48 <option value="">Yes</option> 50 <option value="">Yes</option>
49 <option value="-n">No</option> 51 <option value="-n">No</option>
50 </param> 52 </param>
54 <option value="-C">Output only non-clipped sequences (i.e. sequences which did not contained the adapter)</option> 56 <option value="-C">Output only non-clipped sequences (i.e. sequences which did not contained the adapter)</option>
55 <option value="">Output both clipped and non-clipped sequences</option> 57 <option value="">Output both clipped and non-clipped sequences</option>
56 </param> 58 </param>
57 </inputs> 59 </inputs>
58 <outputs> 60 <outputs>
59 <data format_source="input" name="output" metadata_source="input" /> 61 <data name="output" format_source="input" metadata_source="input" />
60 </outputs> 62 </outputs>
61 <tests> 63 <tests>
62 <test> 64 <test>
63 <param name="input" value="fastx_clipper1.fastq" ftype="fastqsolexa"/> 65 <param name="input" value="fastx_clipper1.fastq" ftype="fastqsolexa"/>
64 <param name="maxmismatches" value="2" /> 66 <param name="maxmismatches" value="2" />
69 <param name="KEEP_N" value="-n" /> 71 <param name="KEEP_N" value="-n" />
70 <param name="DISCARD_OPTIONS" value="-c" /> 72 <param name="DISCARD_OPTIONS" value="-c" />
71 <output name="output" ftype="fastqsolexa" file="fastx_clipper1a.out" /> 73 <output name="output" ftype="fastqsolexa" file="fastx_clipper1a.out" />
72 </test> 74 </test>
73 </tests> 75 </tests>
74 <help> 76 <help><![CDATA[
75 **What it does** 77 **What it does**
76 78
77 This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file. 79 This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file.
78 80
79 -------- 81 --------
95 ------ 97 ------
96 98
97 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. 99 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
98 100
99 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ 101 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
100 </help> 102 ]]></help>
103 <expand macro="citations" />
101 </tool> 104 </tool>