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"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
author qfabrepo
date Mon, 14 Sep 2020 04:50:28 +0000
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1 <tool id="pearStat" name="PEAR Statistics" version="1.0.0">
2 <description>Generate paired-end reads overlap Statistic from PEAR log file</description>
3 <version_command>
4 python ${__tool_directory__}/pear_stats.py --version
5 </version_command>
6 <command detect_errors="aggressive"><![CDATA[
7 #set files=""
8 #for $index,$file in enumerate($input):
9 #set $files += str($file)+","
10 #end for
11 #set $files=$files[:-1]
12
13 #set names=','.join( [ str( $name ) for $name in $input.keys() ])
14
15 python $__tool_directory__/pear_stats.py -i "$files" -s "$names" -o $output
16 ]]> </command>
17 <inputs>
18 <param name="input" type="data_collection" format="txt" collection_type="list" label="PEAR LOG FILE"/>
19 </inputs>
20 <outputs>
21 <!--<data format="tabular" name="output" label="${tool.name}.${input.display_name}"/>-->
22 <data format="tabular" name="output" label="${tool.name}.log"/>
23 </outputs>
24 <tests>
25 <test>
26 <param name="input">
27 <collection type="list">
28 <element name="F3D0" value="F3D0.log" />
29 <element name="F3D1" value="F3D1.log" />
30 </collection>
31 </param>
32 <output name="output" file="test_output.txt"/>
33 </test>
34 </tests>
35
36 <help>
37 ** what it does **
38
39 Creates summary log file by extracting "Assembled reads", "Discarded reads" and "Not assembled reads" from PEAR_ log.
40
41 .. _PEAR: https://sco.h-its.org/exelixis/web/software/pear/doc.html
42
43 -----
44
45 =======
46 Example
47 =======
48
49 PEAR v0.9.6 [January 15, 2015]
50
51 Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR
52 Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593
53
54 ==================================== =======================================
55 Field Parameter and output
56 ------------------------------------ ---------------------------------------
57 Forward reads file.................: /mnt/galaxy/files/014/dataset_14938.dat
58 Reverse reads file.................: /mnt/galaxy/files/014/dataset_14939.dat
59 PHRED..............................: 33
60 Using empirical frequencies........: NO
61 Statistical method.................: OES
62 Maximum assembly length............: 999999
63 Minimum assembly length............: 50
64 p-value............................: 0.010000
65 Quality score threshold (trimming).: 0
66 Minimum read size after trimming...: 1
67 Maximal ratio of uncalled bases....: 1.000000
68 Minimum overlap....................: 10
69 Scoring method.....................: Scaled score
70 Threads............................: 2
71
72 Allocating memory..................: 200,000,000 bytes
73 Assemblying reads: 0%
74 Assemblying reads: 100%
75
76 Assembled reads ...................: 906 / 990 (91.515%)
77 Discarded reads ...................: 0 / 990 (0.000%)
78 Not assembled reads ...............: 84 / 990 (8.485%)
79 Assembled reads file...............: pear.assembled.fastq
80 Discarded reads file...............: pear.discarded.fastq
81 Unassembled forward reads file.....: pear.unassembled.forward.fastq
82 Unassembled reverse reads file.....: pear.unassembled.reverse.fastq
83 ==================================== =======================================
84
85
86 -----
87
88 =========
89 Resources
90 =========
91
92 **Wrapper Authors**
93
94 QFAB Bioinformatics (support@qfab.org)
95
96 </help>
97 <citations>
98 <citation type="doi">10.1093/bioinformatics/btt593</citation>
99 </citations>
100 </tool>