Mercurial > repos > devteam > fastq_groomer

annotate fastq_groomer.xml @ 4:dafabb4c2037 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_groomer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
author devteam
date Fri, 01 Nov 2019 13:16:58 -0400
parents bbc72602f69f
children 4fda2184efa5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
1 <tool id="fastq_groomer" name="FASTQ Groomer" version="1.1.1">
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
2 <description>convert between various FASTQ quality formats</description>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
3 <requirements>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
5 </requirements>
4
dafabb4c2037 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 3
diff changeset
6 <edam_topics>
dafabb4c2037 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 3
diff changeset
7 <edam_topic>topic_0622</edam_topic>
dafabb4c2037 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 3
diff changeset
8 </edam_topics>
dafabb4c2037 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 3
diff changeset
9 <edam_operations>
dafabb4c2037 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 3
diff changeset
10 <edam_operation>operation_0233</edam_operation>
dafabb4c2037 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 3
diff changeset
11 </edam_operations>
3
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
12 <command><![CDATA[
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
13 gx-fastq-groomer '$input_file'
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
14 #if $input_file.extension.endswith(".gz"):
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
15 #set $suffix = ".gz"
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
16 #elif $input_file.extension.endswith(".bz2"):
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
17 #set $suffix = ".bz2"
0
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
18 #else:
3
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
19 #set $suffix = ""
0
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
20 #end if
3
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
21 $input_type$suffix '$output_file'
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
22 #if $options_type['options_type_selector'] == 'basic':
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
23 #if str($input_type) == 'cssanger':
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
24 cssanger
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
25 #else:
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
26 sanger
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
27 #end if
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
28 ascii summarize_input
0
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
29 #else:
3
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
30 ${options_type.output_type} ${options_type.force_quality_encoding} ${options_type.summarize_input}
0
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
31 #end if
3
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
32 ]]></command>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
33 <inputs>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
34 <param name="input_file" type="data" format="fastq,fastq.gz,fastq.bz2" label="File to groom" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
35 <param name="input_type" type="select" label="Input FASTQ quality scores type">
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
36 <option value="solexa">Solexa</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
37 <option value="illumina">Illumina 1.3-1.7</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
38 <option value="sanger" selected="true">Sanger &amp; Illumina 1.8+</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
39 <option value="cssanger">Color Space Sanger</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
40 </param>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
41 <conditional name="options_type">
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
42 <param name="options_type_selector" type="select" label="Advanced Options">
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
43 <option value="basic" selected="true">Hide Advanced Options</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
44 <option value="advanced">Show Advanced Options</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
45 </param>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
46 <when value="basic" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
47 <when value="advanced">
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
48 <param name="output_type" type="select" label="Output FASTQ quality scores type" help="Galaxy tools are designed to work with the Sanger Quality score format">
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
49 <option value="solexa">Solexa</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
50 <option value="illumina">Illumina 1.3-1.7</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
51 <option value="sanger" selected="true">Sanger</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
52 <option value="cssanger">Color Space Sanger</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
53 <option value="solexa.gz">Solexa (gz compressed)</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
54 <option value="illumina.gz">Illumina 1.3-1.7 (gz compressed)</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
55 <option value="sanger.gz">Sanger (gz compressed - recommended)</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
56 <option value="cssanger.gz">Color Space Sanger (gz compressed)</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
57 <option value="solexa.bz2">Solexa (bz2 compressed)</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
58 <option value="illumina.bz2">Illumina 1.3-1.7 (bz2 compressed)</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
59 <option value="sanger.bz2">Sanger (bz2 compressed)</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
60 <option value="cssanger.bz2">Color Space Sanger (bz2 compressed)</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
61 </param>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
62 <param name="force_quality_encoding" type="select" label="Force Quality Score encoding">
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
63 <option value="None">Use Source Encoding</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
64 <option value="ascii" selected="true">ASCII</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
65 <option value="decimal">Decimal</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
66 </param>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
67 <param name="summarize_input" type="select" label="Summarize input data">
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
68 <option value="summarize_input" selected="true">Summarize Input</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
69 <option value="dont_summarize_input">Do not Summarize Input (faster)</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
70 </param>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
71 </when>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
72 </conditional>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
73 </inputs>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
74 <outputs>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
75 <data name="output_file" format="fastqsanger">
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
76 <change_format>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
77 <when input="input_type" value="cssanger" format="fastqcssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
78 <when input="options_type.output_type" value="solexa" format="fastqsolexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
79 <when input="options_type.output_type" value="illumina" format="fastqillumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
80 <when input="options_type.output_type" value="sanger" format="fastqsanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
81 <when input="options_type.output_type" value="cssanger" format="fastqcssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
82 <when input="options_type.output_type" value="solexa.gz" format="fastqsolexa.gz" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
83 <when input="options_type.output_type" value="illumina.gz" format="fastqillumina.gz" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
84 <when input="options_type.output_type" value="sanger.gz" format="fastqsanger.gz" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
85 <when input="options_type.output_type" value="cssanger.gz" format="fastqcssanger.gz" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
86 <when input="options_type.output_type" value="solexa.bz2" format="fastqsolexa.bz2" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
87 <when input="options_type.output_type" value="illumina.bz2" format="fastqillumina.bz2" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
88 <when input="options_type.output_type" value="sanger.bz2" format="fastqsanger.bz2" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
89 <when input="options_type.output_type" value="cssanger.bz2" format="fastqcssanger.bz2" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
90 </change_format>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
91 </data>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
92 </outputs>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
93 <tests>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
94 <!-- These tests include test files adapted from supplemental material in Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16. -->
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
95 <!-- Test basic options -->
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
96 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
97 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
98 <param name="input_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
99 <param name="options_type_selector" value="basic" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
100 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
101 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
102 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
103 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
104 <param name="input_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
105 <param name="options_type_selector" value="basic" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
106 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
107 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
108 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
109 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
110 <param name="input_type" value="illumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
111 <param name="options_type_selector" value="basic" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
112 <output name="output_file" file="illumina_full_range_as_sanger.fastqsanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
113 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
114 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
115 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
116 <param name="input_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
117 <param name="options_type_selector" value="basic" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
118 <output name="output_file" file="solexa_full_range_as_sanger.fastqsanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
119 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
120 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
121 <param name="input_file" value="sanger_full_range_as_illumina.fastqillumina" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
122 <param name="input_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
123 <param name="options_type_selector" value="basic" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
124 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
125 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
126 <!-- Test grooming from illumina -->
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
127 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
128 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
129 <param name="input_type" value="illumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
130 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
131 <param name="output_type" value="illumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
132 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
133 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
134 <output name="output_file" file="illumina_full_range_original_illumina.fastqillumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
135 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
136 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
137 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
138 <param name="input_type" value="illumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
139 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
140 <param name="output_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
141 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
142 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
143 <output name="output_file" file="illumina_full_range_as_sanger.fastqsanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
144 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
145 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
146 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
147 <param name="input_type" value="illumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
148 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
149 <param name="output_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
150 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
151 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
152 <output name="output_file" file="illumina_full_range_as_solexa.fastqsolexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
153 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
154 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
155 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
156 <param name="input_type" value="illumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
157 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
158 <param name="output_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
159 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
160 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
161 <output name="output_file" file="illumina_full_range_as_cssanger.fastqcssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
162 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
163 <!-- Test grooming from sanger -->
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
164 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
165 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
166 <param name="input_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
167 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
168 <param name="output_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
169 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
170 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
171 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
172 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
173 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
174 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
175 <param name="input_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
176 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
177 <param name="output_type" value="illumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
178 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
179 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
180 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
181 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
182 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
183 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
184 <param name="input_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
185 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
186 <param name="output_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
187 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
188 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
189 <output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
190 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
191 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
192 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
193 <param name="input_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
194 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
195 <param name="output_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
196 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
197 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
198 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
199 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
200 <!-- Test grooming from solexa -->
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
201 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
202 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
203 <param name="input_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
204 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
205 <param name="output_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
206 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
207 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
208 <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
209 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
210 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
211 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
212 <param name="input_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
213 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
214 <param name="output_type" value="illumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
215 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
216 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
217 <output name="output_file" file="solexa_full_range_as_illumina.fastqillumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
218 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
219 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
220 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
221 <param name="input_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
222 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
223 <param name="output_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
224 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
225 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
226 <output name="output_file" file="solexa_full_range_as_sanger.fastqsanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
227 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
228 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
229 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
230 <param name="input_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
231 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
232 <param name="output_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
233 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
234 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
235 <output name="output_file" file="solexa_full_range_as_cssanger.fastqcssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
236 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
237 <!-- Test grooming from cssanger -->
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
238 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
239 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
240 <param name="input_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
241 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
242 <param name="output_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
243 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
244 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
245 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
246 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
247 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
248 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
249 <param name="input_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
250 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
251 <param name="output_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
252 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
253 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
254 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
255 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
256 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
257 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
258 <param name="input_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
259 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
260 <param name="output_type" value="illumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
261 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
262 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
263 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
264 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
265 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
266 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
267 <param name="input_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
268 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
269 <param name="output_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
270 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
271 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
272 <output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
273 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
274 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
275 <param name="input_file" value="sanger_full_range_as_cssanger_adapter_base_with_quality_score.fastqcssanger_fake_score" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
276 <param name="input_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
277 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
278 <param name="output_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
279 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
280 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
281 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
282 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
283 <!-- Test fastq with line wrapping -->
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
284 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
285 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
286 <param name="input_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
287 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
288 <param name="output_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
289 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
290 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
291 <output name="output_file" file="wrapping_as_sanger.fastqsanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
292 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
293 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
294 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
295 <param name="input_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
296 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
297 <param name="output_type" value="illumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
298 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
299 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
300 <output name="output_file" file="wrapping_as_illumina.fastqillumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
301 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
302 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
303 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
304 <param name="input_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
305 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
306 <param name="output_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
307 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
308 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
309 <output name="output_file" file="wrapping_as_solexa.fastqsolexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
310 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
311 <!-- Test forcing quality score encoding -->
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
312 <!-- Sanger, range 0 - 93 -->
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
313 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
314 <param name="input_file" value="sanger_full_range_as_decimal_sanger.fastqsanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
315 <param name="input_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
316 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
317 <param name="output_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
318 <param name="force_quality_encoding" value="ascii" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
319 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
320 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
321 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
322 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
323 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
324 <param name="input_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
325 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
326 <param name="output_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
327 <param name="force_quality_encoding" value="decimal" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
328 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
329 <output name="output_file" file="sanger_full_range_as_decimal_sanger.fastqsanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
330 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
331 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
332 <param name="input_file" value="sanger_full_range_as_tab_decimal_sanger.fastqsanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
333 <param name="input_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
334 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
335 <param name="output_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
336 <param name="force_quality_encoding" value="ascii" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
337 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
338 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
339 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
340 <!-- Solexa, range -5 - 62 -->
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
341 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
342 <param name="input_file" value="solexa_full_range_as_decimal_solexa.fastqsolexa" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
343 <param name="input_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
344 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
345 <param name="output_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
346 <param name="force_quality_encoding" value="ascii" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
347 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
348 <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
349 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
350 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
351 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
352 <param name="input_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
353 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
354 <param name="output_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
355 <param name="force_quality_encoding" value="decimal" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
356 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
357 <output name="output_file" file="solexa_full_range_as_decimal_solexa.fastqsolexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
358 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
359 <!-- compressed formats -->
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
360 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
361 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger.gz" ftype="fastq.gz" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
362 <param name="input_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
363 <param name="options_type_selector" value="basic" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
364 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" decompress="true" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
365 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
366 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
367 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger.bz2" ftype="fastq.bz2" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
368 <param name="input_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
369 <param name="options_type_selector" value="basic" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
370 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" decompress="true" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
371 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
372 </tests>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
373 <help><![CDATA[
0
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
374 **What it does**
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
375
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
376 This tool offers several conversions options relating to the FASTQ format.
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
377
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
378 When using *Basic* options, the output will be *sanger* formatted or *cssanger* formatted (when the input is Color Space Sanger).
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
379
3
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
380 When converting, if a quality score falls outside of the target score range, it will be coerced to the closest available value (i.e. the minimum or maximum).
0
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
381
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
382 When converting between Solexa and the other formats, quality scores are mapped between Solexa and PHRED scales using the equations found in `Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.`_
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
383
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
384 When converting between color space (csSanger) and base/sequence space (Sanger, Illumina, Solexa) formats, adapter bases are lost or gained; if gained, the base 'G' is used as the adapter. You cannot convert a color space read to base space if there is no adapter present in the color space sequence. Any masked or ambiguous nucleotides in base space will be converted to 'N's when determining color space encoding.
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
385
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
386 -----
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
387
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
388 **Quality Score Comparison**
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
389
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
390 ::
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
391
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
392 SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
393 ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
394 ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
3
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
395 !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
0
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
396 | | | | | |
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
397 33 59 64 73 104 126
3
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
398
0
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
399 S - Sanger Phred+33, 93 values (0, 93) (0 to 60 expected in raw reads)
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
400 I - Illumina 1.3 Phred+64, 62 values (0, 62) (0 to 40 expected in raw reads)
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
401 X - Solexa Solexa+64, 67 values (-5, 62) (-5 to 40 expected in raw reads)
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
402
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
403 Diagram adapted from http://en.wikipedia.org/wiki/FASTQ_format
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
404
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
405 .. class:: infomark
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
406
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
407 Output from Illumina 1.8+ pipelines are Sanger encoded.
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
408
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
409 ------
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
410
3
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
411 .. _Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.: https://doi.org/10.1093/nar/gkp1137
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
412 ]]></help>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
413 <citations>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
414 <citation type="doi">10.1093/bioinformatics/btq281</citation>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
415 </citations>
0
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
416 </tool>