Mercurial > repos > devteam > fastx_collapser
comparison fastx_collapser.xml @ 2:421f0af4ee95 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 12:39:04 -0500 |
parents | 13c2d9e8c6d5 |
children | 7ce1891db6f5 |
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1:13c2d9e8c6d5 | 2:421f0af4ee95 |
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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 <param 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> |