Mercurial > repos > devteam > fastx_quality_statistics
comparison fastx_quality_statistics.xml @ 3:59003d0543cd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author | iuc |
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date | Tue, 08 May 2018 13:28:00 -0400 |
parents | 7306ec78632a |
children | cc0fd298cc17 |
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2:7306ec78632a | 3:59003d0543cd |
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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> |