Mercurial > repos > veg > qfilt

annotate qfilt.xml @ 1:2ab93e1952c5 draft default tip

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-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
author veg
date Wed, 18 Apr 2018 16:53:05 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
1 <?xml version="1.0"?>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
2 <tool id="qfilt" version="1.0.0" name="qfilt">
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
3 <description>filter sequencing data using simple heuristics</description>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
4 <requirements>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
5 <requirement type="package" version="0.0.1">qfilt</requirement>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
6 </requirements>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
7 <stdio>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
8 <exit_code range="1:"/>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
9 </stdio>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
10 <command><![CDATA[
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
11 qfilt -o '$filtered_output'
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
12 #if str($options.advanced) == 'advanced':
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
13 -q $options.qscore -l $options.length
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
14 -s $options.split
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
15 #if $options.replace and $options.remove:
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
16 -P $options.replace -R $options.remove
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
17 #elif $options.mode:
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
18 -m $options.mode
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
19 #end if
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
20 #if $options.prefix:
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
21 -t $options.mismatch
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
22 -T $options.prefix
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
23 #end if
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
24 -f $options.format
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
25 $options.tolerate_homopolymeric $options.tolerate_ambiguous
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
26 #end if
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
27 -Q '$input_fastq'
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
28 ]]></command>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
29 <inputs>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
30
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
31 <param name="input_fastq" argument="-Q" type="data" format="fastq" label="Input FASTA" help="FASTQ File" />
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
32
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
33 <conditional name="options">
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
34
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
35 <param name="advanced" type="select" label="Additional options">
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
36 <option value="defaults">Use defaults</option>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
37 <option value="advanced">Specify additional parameters</option>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
38 </param>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
39
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
40 <when value="defaults"/>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
41
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
42 <when value="advanced">
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
43 <param name="qscore" argument="-q" type="integer" value="20" label="QScore" help="minimum per-base quality score below which a read will be split or truncated" />
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
44 <param name="length" argument="-l" type="integer" value="50" label="Length" help="minimum retained fragment LENGTH" />
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
45 <param name="mode" argument="-m" type="integer" value="0" label="Mode" help="MODE is a 3-bitmask (an integer in [0-7], default=0)" />
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
46 <param name="split" argument="-s" type="text" label="Split" help="when encountering a low q-score, split instead of truncate" />
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
47 <param name="tolerate_homopolymeric" argument="-p" type="boolean" truevalue="-p" falsevalue="" label="Tolerate Homopolymeric" help="tolerate low q-score homopolymeric regions" />
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
48 <param name="tolerate_ambiguous" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Tolerate Ambiguous" help="tolerate low q-score ambiguous nucleotides" />
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
49 <param name="replace" argument="-P" type="text" label="Replace" help="rather than splitting or truncating, replace low quality bases with CHAR this option OVERRIDES all -m mode options" />
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
50 <param name="remove" argument="-R" type="text" label="Remove" help="rather than splitting or truncating, remove reads which contain more than COUNT low quality bases this option only works in COMBINATION with the -P (punch) option" />
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
51 <param name="prefix" argument="-T" type="text" label="Prefix" help="if supplied, only reads with this PREFIX are retained, and the PREFIX is stripped from each contributing read" />
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
52 <param name="mismatch" argument="-t" type="integer" value="0" label="Mismatch" help="if PREFIX is supplied, prefix matching tolerates at most MISMATCH mismatches" />
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
53 <param name="format" argument="-f" type="select" label="Format" help="output in FASTA or FASTQ format (default=FASTA)" >
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
54 <option value="FASTA">FASTA</option>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
55 <option value="FASTQ">FASTQ</option>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
56 </param>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
57 </when>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
58
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
59 </conditional>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
60
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
61 </inputs>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
62 <outputs>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
63 <data format="fasta" name="filtered_output"/>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
64 </outputs>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
65 <tests>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
66 <test>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
67 <param name="input_fastq" value="qfilt-in1.fastq" />
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
68 <output file="qfilt-out1.fa" ftype="fasta" name="filtered_output" />
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
69 </test>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
70 <test>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
71 <param name="input_fastq" value="qfilt-in1.fastq" />
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
72 <param name="advanced" value="advanced" />
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
73 <param name="tolerate_homopolymeric" value="False" />
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
74 <output file="qfilt-out2.fa" ftype="fasta" name="filtered_output" />
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
75 </test>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
76 </tests>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
77 <help><![CDATA[
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
78 qfilt
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
79 =====
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
80
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
81 This simple program is meant to filter sequencing data,
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
82 optionally removing or splitting reads with poor quality scores
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
83 and to optionally _only_ retain fragments from reads that are tagged with a given 5' sequence.
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
84
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
85 ### OUTPUT: ####
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
86
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
87 #### stderr: ####
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
88
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
89 run settings:
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
90 input fasta: data/test.fna
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
91 input qual: data/test.qual
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
92 min q-score: 15
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
93 min fragment length: 30
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
94 run mode: 0 (truncate/don't tolerate homopolymers/don't tolerate ambigs)
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
95 5' tag: ATATCGCGAGGA
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
96 max tag mismatches: 0
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
97
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
98 run summary:
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
99 total bases : 29570
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
100 original reads : 305
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
101 q10 : 0.995502
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
102 q20 : 0.860298
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
103 q30 : 0.728745
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
104 mean q-score : 33.2273
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
105 contributing reads: 5
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
106 retained fragments: 5
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
107
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
108 original read length distribution:
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
109 mean: 96.9508
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
110 median: 77
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
111 variance 3743.03
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
112 standard deviation: 61.1803
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
113 min: 49
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
114 2.5%: 54
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
115 97.5%: 332
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
116 max: 497
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
117
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
118 retained fragment length distribution:
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
119 mean: 41
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
120 median: 37
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
121 variance 72.5
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
122 standard deviation: 8.51469
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
123 min: 33
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
124 2.5%: 33
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
125 97.5%: 54
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
126 max: 54
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
127
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
128 #### stdout: ####
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
129
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
130 >GM98SRO01B77KU rank=0000671 x=796.0 y=1996.0 length=58
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
131 CCACGCGTATCGATGTCGACTTTTTTTTCTTTTCTTACATAGTAG
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
132 >GM98SRO01BA3RP rank=0000953 x=419.5 y=1603.5 length=87
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
133 CTGATGCTGCACCAACTGTACTCCCTCGCGATA
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
134 >GM98SRO01E1BKW rank=0001233 x=1948.0 y=846.0 length=66
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
135 TACAGTTGGTGCAGCATCAGAAAAGTACGACATCGATACGCGTGGTCCTCGCGA
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
136 >GM98SRO01DVVNY rank=0001304 x=1476.0 y=636.5 length=84
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
137 ACGGCTGATGCTGCACCAACTGTACTCCCTCGCGATA
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
138 >GM98SRO01D6FIX rank=0001416 x=1596.0 y=1415.0 length=91
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
139 CGGCTGATGCTGCACCAACTGTACTCCCTCGCGATA
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
140 ]]></help>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
141 <citations>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
142 <citation type="bibtex">
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
143 @UNPUBLISHED{spond,
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
144 author = "Sergei Kosakovsky Pond",
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
145 title = "HyPhy: Hypothesis Testing using Phylogenies",
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
146 year = "2000",
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
147 note = "http://hyphy.org/",
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
148 url = "http://hyphy.org/"}
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
149 </citation>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
150 </citations>
2ab93e1952c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit c9f251e99e052ab4d87ed5fd89e466cdf387742b-dirty
veg
parents:
diff changeset
151 </tool>