Mercurial > repos > devteam > fastq_stats

comparison fastq_stats.xml @ 2:e2cf940128d5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
author devteam
date Sat, 30 Sep 2017 13:55:30 -0400
parents daaf552153fe
children b1cea1b2fcd0
comparison
equal deleted inserted replaced
1:daaf552153fe 2:e2cf940128d5
1 <tool id="fastq_stats" name="FASTQ Summary Statistics" version="1.0.0"> 1 <tool id="fastq_stats" name="FASTQ Summary Statistics" version="1.1.1">
2 <description>by column</description> 2 <description>by column</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> 4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python">fastq_stats.py '$input_file' '$output_file' '${input_file.extension[len( 'fastq' ):]}'</command> 6 <command><![CDATA[
7 <inputs> 7 gx-fastq-stats '$input_file' '$output_file' '${input_file.extension[len('fastq'):]}'
8 <param name="input_file" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqcssanger" label="FASTQ File"/> 8 ]]></command>
9 </inputs> 9 <inputs>
10 <outputs> 10 <param name="input_file" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqcssanger,fastqsanger.gz,fastqillumina.gz,fastqsolexa.gz,fastqcssanger.gz,fastqsanger.bz2,fastqillumina.bz2,fastqsolexa.bz2,fastqcssanger.bz2" label="FASTQ File"/>
11 <data name="output_file" format="tabular" /> 11 </inputs>
12 </outputs> 12 <outputs>
13 <tests> 13 <data name="output_file" format="tabular" />
14 <test> 14 </outputs>
15 <param name="input_file" value="fastq_stats1.fastq" ftype="fastqsanger" /> 15 <tests>
16 <output name="output_file" file="fastq_stats_1_out.tabular" /> 16 <test>
17 </test> 17 <param name="input_file" value="fastq_stats1.fastq" ftype="fastqsanger" />
18 </tests> 18 <output name="output_file" file="fastq_stats_1_out.tabular" />
19 <help> 19 </test>
20 </tests>
21 <help><![CDATA[
20 **What is does** 22 **What is does**
21 23
22 This tool creates summary statistics on a FASTQ file. 24 This tool creates summary statistics on a FASTQ file.
23 25
24 .. class:: infomark 26 .. class:: infomark
25 27
26 **TIP:** This statistics report can be used as input for the **Boxplot** tools. 28 **TIP:** This statistics report can be used as input for the **Boxplot** tools.
27 29
51 * Other_Count = Comma separated count of other nucleotides found in this column. 53 * Other_Count = Comma separated count of other nucleotides found in this column.
52 54
53 For example:: 55 For example::
54 56
55 #column count min max sum mean Q1 med Q3 IQR lW rW outliers A_Count C_Count G_Count T_Count N_Count other_bases other_base_count 57 #column count min max sum mean Q1 med Q3 IQR lW rW outliers A_Count C_Count G_Count T_Count N_Count other_bases other_base_count
56 1 14336356 2 33 450600675 31.4306281875 32.0 33.0 33.0 1.0 31 33 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30 4482314 2199633 4425957 3208745 19707 58 1 14336356 2 33 450600675 31.4306281875 32.0 33.0 33.0 1.0 31 33 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30 4482314 2199633 4425957 3208745 19707
57 2 14336356 2 34 441135033 30.7703737965 30.0 33.0 33.0 3.0 26 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25 4419184 2170537 4627987 3118567 81 59 2 14336356 2 34 441135033 30.7703737965 30.0 33.0 33.0 3.0 26 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25 4419184 2170537 4627987 3118567 81
58 3 14336356 2 34 433659182 30.2489127642 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4310988 2941988 3437467 3645784 129 60 3 14336356 2 34 433659182 30.2489127642 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4310988 2941988 3437467 3645784 129
59 4 14336356 2 34 433635331 30.2472490917 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4110637 3007028 3671749 3546839 103 61 4 14336356 2 34 433635331 30.2472490917 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4110637 3007028 3671749 3546839 103
60 5 14336356 2 34 432498583 30.167957813 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4348275 2935903 3293025 3759029 124 62 5 14336356 2 34 432498583 30.167957813 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4348275 2935903 3293025 3759029 124
61 63
62 ----- 64 -----
63 65
64 .. class:: warningmark 66 .. class:: warningmark
65 67
66 Adapter bases in color space reads are excluded from statistics. 68 Adapter bases in color space reads are excluded from statistics.
67 69 ]]></help>
68 ------ 70 <citations>
69 71 <citation type="doi">10.1093/bioinformatics/btq281</citation>
70 </help> 72 </citations>
71
72 <citations>
73 <citation type="doi">10.1093/bioinformatics/btq281</citation>
74 </citations>
75
76 </tool> 73 </tool>