Mercurial > repos > devteam > fastx_artifacts_filter
comparison fastx_artifacts_filter.xml @ 3:dd3737e40dce draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author | iuc |
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date | Tue, 08 May 2018 13:27:02 -0400 |
parents | 09070cacefd8 |
children | 567d5b3c52b1 |
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2:09070cacefd8 | 3:dd3737e40dce |
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1 <tool id="cshl_fastx_artifacts_filter" version="1.0.0" name="Remove sequencing artifacts"> | 1 <tool id="cshl_fastx_artifacts_filter" version="1.0.1" name="Remove sequencing artifacts"> |
2 <description></description> | 2 <description></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 < '$input' | fastx_artifacts_filter -v -o '$output' | 8 @CATS@ fastx_artifacts_filter |
9 #if $input.ext == "fastqsanger": | 9 -v |
10 -Q 33 | 10 -o '$output' |
11 #end if | 11 @FQQUAL@ |
12 ]]> | 12 ]]></command> |
13 </command> | |
14 | 13 |
15 <inputs> | 14 <inputs> |
16 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to filter" /> | 15 <expand macro="fastx_input" /> |
17 </inputs> | 16 </inputs> |
18 <outputs> | 17 <outputs> |
19 <data format_source="input" name="output" metadata_source="input" /> | 18 <data name="output" format_source="input" metadata_source="input" /> |
20 </outputs> | 19 </outputs> |
21 <tests> | 20 <tests> |
22 <test> | 21 <test> |
23 <!-- Filter FASTA file --> | 22 <!-- Filter FASTA file --> |
24 <param name="input" value="fastx_artifacts1.fasta" /> | 23 <param name="input" value="fastx_artifacts1.fasta" /> |
28 <!-- Filter FASTQ file --> | 27 <!-- Filter FASTQ file --> |
29 <param name="input" value="fastx_artifacts2.fastq" ftype="fastqsanger" /> | 28 <param name="input" value="fastx_artifacts2.fastq" ftype="fastqsanger" /> |
30 <output name="output" ftype="fastqsanger" file="fastx_artifacts2.out" /> | 29 <output name="output" ftype="fastqsanger" file="fastx_artifacts2.out" /> |
31 </test> | 30 </test> |
32 </tests> | 31 </tests> |
33 <help> | 32 <help><![CDATA[ |
34 **What it does** | 33 **What it does** |
35 | 34 |
36 This tool filters sequencing artifacts (reads with all but 3 identical bases). | 35 This tool filters sequencing artifacts (reads with all but 3 identical bases). |
37 | 36 |
38 -------- | 37 -------- |
85 ------ | 84 ------ |
86 | 85 |
87 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | 86 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. |
88 | 87 |
89 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | 88 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ |
90 </help> | 89 ]]></help> |
90 <expand macro="citations" /> | |
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> |