Mercurial > repos > devteam > fastx_artifacts_filter
comparison fastx_artifacts_filter.xml @ 2:09070cacefd8 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
---|---|
date | Wed, 11 Nov 2015 12:38:23 -0500 |
parents | c8808979ba33 |
children | dd3737e40dce |
comparison
equal
deleted
inserted
replaced
1:c8808979ba33 | 2:09070cacefd8 |
---|---|
1 <tool id="cshl_fastx_artifacts_filter" version="1.0.0" name="Remove sequencing artifacts"> | 1 <tool id="cshl_fastx_artifacts_filter" version="1.0.0" name="Remove sequencing artifacts"> |
2 <description></description> | 2 <description></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 '$input' | fastx_artifacts_filter -v -o "$output" | 6 <command> |
7 <![CDATA[ | |
8 zcat -f < '$input' | fastx_artifacts_filter -v -o '$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,fastqillumina" name="input" type="data" label="Library to filter" /> | 16 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to filter" /> |
14 | 17 </inputs> |
15 </inputs> | 18 <outputs> |
16 | 19 <data format_source="input" name="output" metadata_source="input" /> |
17 <tests> | 20 </outputs> |
18 <test> | 21 <tests> |
19 <!-- Filter FASTA file --> | 22 <test> |
20 <param name="input" value="fastx_artifacts1.fasta" /> | 23 <!-- Filter FASTA file --> |
21 <param name="output" file="fastx_artifacts1.out" /> | 24 <param name="input" value="fastx_artifacts1.fasta" /> |
22 </test> | 25 <output name="output" ftype="fasta" file="fastx_artifacts1.out" /> |
23 <test> | 26 </test> |
24 <!-- Filter FASTQ file --> | 27 <test> |
25 <param name="input" value="fastx_artifacts2.fastq" ftype="fastqsanger" /> | 28 <!-- Filter FASTQ file --> |
26 <param name="output" file="fastx_artifacts2.out" /> | 29 <param name="input" value="fastx_artifacts2.fastq" ftype="fastqsanger" /> |
27 </test> | 30 <output name="output" ftype="fastqsanger" file="fastx_artifacts2.out" /> |
28 </tests> | 31 </test> |
29 | 32 </tests> |
30 <outputs> | 33 <help> |
31 <data format="input" name="output" metadata_source="input" /> | |
32 </outputs> | |
33 <help> | |
34 **What it does** | 34 **What it does** |
35 | 35 |
36 This tool filters sequencing artifacts (reads with all but 3 identical bases). | 36 This tool filters sequencing artifacts (reads with all but 3 identical bases). |
37 | 37 |
38 -------- | 38 -------- |
79 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | 79 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
80 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | 80 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
81 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAA | 81 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAA |
82 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAA | 82 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAA |
83 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAA | 83 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAA |
84 | 84 |
85 ------ | 85 ------ |
86 | 86 |
87 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | 87 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. |
88 | 88 |
89 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | 89 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ |
90 </help> | 90 </help> |
91 <!-- FASTX-Artifacts-filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> | 91 <!-- FASTX-Artifacts-filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> |
92 </tool> | 92 </tool> |