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comparison fastx_collapser.xml @ 2:17bfc147c9ea draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:41:05 -0400
parents 460c78dbadf8
children 7bda0f25191f
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1:460c78dbadf8 2:17bfc147c9ea
1 <tool id="cshl_fastx_collapser" version="1.0.0" name="Collapse"> 1 <tool id="cshl_fastx_collapser" version="1.0.0" name="Collapse">
2 <description>sequences</description> 2 <description>sequences</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
5 </requirements> 5 </requirements>
6 <command>zcat -f '$input' | fastx_collapser -v -o '$output' 6 <command>
7 <![CDATA[
8 zcat -f < '$input' | fastx_collapser -v -o '$output'
7 #if $input.ext == "fastqsanger": 9 #if $input.ext == "fastqsanger":
8 -Q 33 10 -Q 33
9 #end if 11 #end if
10 </command> 12 ]]>
13 </command>
11 14
12 <inputs> 15 <inputs>
13 <param format="fasta,fastqsanger,fastqsolexa" name="input" type="data" label="Library to collapse" /> 16 <param format="fasta,fastqsanger,fastqsolexa" name="input" type="data" label="Library to collapse" />
14 </inputs> 17 </inputs>
15 18 <outputs>
16 <!-- The order of sequences in the test output differ between 32 bit and 64 bit machines. 19 <data format="fasta" name="output" metadata_source="input" />
17 <tests> 20 </outputs>
18 <test> 21 <!-- The order of sequences in the test output differ between 32 bit and 64 bit machines.
19 <param name="input" value="fasta_collapser1.fasta" /> 22 <tests>
20 <output name="output" file="fasta_collapser1.out" /> 23 <test>
21 </test> 24 <param name="input" value="fasta_collapser1.fasta" />
22 </tests> 25 <param name="output" file="fasta_collapser1.out" />
26 </test>
27 </tests>
23 --> 28 -->
24 <outputs> 29 <help>
25 <data format="fasta" name="output" metadata_source="input" />
26 </outputs>
27 <help>
28
29 **What it does** 30 **What it does**
30 31
31 This tool collapses identical sequences in a FASTA file into a single sequence. 32 This tool collapses identical sequences in a FASTA file into a single sequence.
32 33
33 -------- 34 --------
34 35
35 **Example** 36 **Example**
36 37
37 Example Input File (Sequence "ATAT" appears multiple times):: 38 Example Input File (Sequence "ATAT" appears multiple times)::
38 39
39 >CSHL_2_FC0042AGLLOO_1_1_605_414 40 >CSHL_2_FC0042AGLLOO_1_1_605_414
40 TGCG 41 TGCG
41 >CSHL_2_FC0042AGLLOO_1_1_537_759 42 >CSHL_2_FC0042AGLLOO_1_1_537_759
42 ATAT 43 ATAT
63 TGGC 64 TGGC
64 >4-1 65 >4-1
65 TGAG 66 TGAG
66 >5-1 67 >5-1
67 TTCA 68 TTCA
68 69
69 .. class:: infomark 70 .. class:: infomark
70 71
71 Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded. 72 Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded.
72 73
73 The output sequence name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value. 74 The output sequence name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value.
74 75
75 The following output:: 76 The following output::
76 77
83 ------ 84 ------
84 85
85 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. 86 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
86 87
87 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ 88 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
88 89 </help>
89 </help>
90 </tool> 90 </tool>