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comparison fastx_quality_statistics.xml @ 3:29924496aeb0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 12:52:11 -0400
parents 76cefe061c3d
children 0674d92802bf
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2:76cefe061c3d 3:29924496aeb0
1 <tool id="cshl_fastx_quality_statistics" version="1.0.0" name="Compute quality statistics"> 1 <tool id="cshl_fastx_quality_statistics" version="1.0.1" name="Compute quality statistics">
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 < '$input' | fastx_quality_stats -o '$output' -Q 33 8 @CATS@ fastx_quality_stats
9 ]]> 9 -o '$output'
10 </command> 10 @FQQUAL@
11 ]]></command>
11 12
12 <inputs> 13 <inputs>
13 <param format="fastqsanger" name="input" type="data" label="Library to analyse" /> 14 <expand macro="fastq_input" />
14 </inputs> 15 </inputs>
15 <outputs> 16 <outputs>
16 <data format="txt" name="output" metadata_source="input" /> 17 <data name="output" format="txt" metadata_source="input" />
17 </outputs> 18 </outputs>
18 <tests> 19 <tests>
19 <test> 20 <test>
20 <param name="input" value="fastq_stats1.fastq" ftype="fastqsanger"/> 21 <param name="input" value="fastq_stats1.fastq" ftype="fastqsanger"/>
21 <output name="output" file="fastq_stats1.out" /> 22 <output name="output" file="fastq_stats1.out" />
22 </test> 23 </test>
23 </tests> 24 </tests>
24 <help> 25 <help><![CDATA[
25 **What it does** 26 **What it does**
26 27
27 Creates quality statistics report for the given Solexa/FASTQ library. 28 Creates quality statistics report for the given Solexa/FASTQ library.
28 29
29 .. class:: infomark 30 .. class:: infomark
50 * C_Count = Count of 'C' nucleotides found in this column. 51 * C_Count = Count of 'C' nucleotides found in this column.
51 * G_Count = Count of 'G' nucleotides found in this column. 52 * G_Count = Count of 'G' nucleotides found in this column.
52 * T_Count = Count of 'T' nucleotides found in this column. 53 * T_Count = Count of 'T' nucleotides found in this column.
53 * N_Count = Count of 'N' nucleotides found in this column. 54 * N_Count = Count of 'N' nucleotides found in this column.
54 55
55
56 For example:: 56 For example::
57 57
58 1 6362991 -4 40 250734117 39.41 40 40 40 0 40 40 1396976 1329101 678730 2958184 0 58 1 6362991 -4 40 250734117 39.41 40 40 40 0 40 40 1396976 1329101 678730 2958184 0
59 2 6362991 -5 40 250531036 39.37 40 40 40 0 40 40 1786786 1055766 1738025 1782414 0 59 2 6362991 -5 40 250531036 39.37 40 40 40 0 40 40 1786786 1055766 1738025 1782414 0
60 3 6362991 -5 40 248722469 39.09 40 40 40 0 40 40 2296384 984875 1443989 1637743 0 60 3 6362991 -5 40 248722469 39.09 40 40 40 0 40 40 2296384 984875 1443989 1637743 0
64 ------ 64 ------
65 65
66 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. 66 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
67 67
68 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ 68 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
69 </help> 69 ]]></help>
70 <expand macro="citations" />
70 <!-- FASTQ-Statistics is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> 71 <!-- FASTQ-Statistics is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
71 </tool> 72 </tool>