Mercurial > repos > devteam > fastq_groomer

annotate fastq_groomer.xml @ 6:3213285ee5d2 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
author iuc
date Fri, 04 Oct 2024 10:33:13 +0000
parents 4fda2184efa5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
3213285ee5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
iuc
parents: 5
diff changeset
1 <tool id="fastq_groomer" name="FASTQ Groomer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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
2 <description>convert between various FASTQ quality formats</description>
5
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
3 <macros>
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
4 <import>macros.xml</import>
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
5 </macros>
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>
6
3213285ee5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
iuc
parents: 5
diff changeset
12 <expand macro="requirements"/>
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
13 <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
14 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
15 #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
16 #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
17 #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
18 #set $suffix = ".bz2"
0
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
19 #else:
5
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
20 #set $suffix = ""
0
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
21 #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
22 $input_type$suffix '$output_file'
5
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
23 #if $options_type.options_type_selector == 'basic':
3
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
24 #if str($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
25 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
26 #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
27 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
28 #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
29 ascii summarize_input
0
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
30 #else:
5
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
31 ${options_type.output_type} ${options_type.force_quality_encoding} ${options_type.summarize_input} ${options_type.fix_id}
0
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
32 #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
33 ]]></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
34 <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
35 <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
36 <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
37 <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
38 <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
39 <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
40 <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
41 </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
42 <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
43 <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
44 <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
45 <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
46 </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
47 <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
48 <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
49 <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
50 <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
51 <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
52 <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
53 <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
54 <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
55 <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
56 <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
57 <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
58 <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
59 <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
60 <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
61 <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
62 </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
63 <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
64 <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
65 <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
66 <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
67 </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
68 <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
69 <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
70 <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
71 </param>
5
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
72 <param name="fix_id" type="boolean" label="Fix inconsistent identifiers"
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
73 truevalue="--fix-id" falsevalue="--no-fix-id" checked="true">
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
74 </param>
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
75 </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
76 </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
77 </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
78 <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
79 <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
80 <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
81 <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
82 <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
83 <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
84 <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
85 <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
86 <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
87 <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
88 <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
89 <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
90 <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
91 <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
92 <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
93 <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
94 </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
95 </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
96 </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
97 <tests>
5
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
98 <!-- Test fix-id by default -->
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
99 <test>
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
100 <param name="input_file" value="fastq_invalid-line3" ftype="fastq" />
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
101 <param name="input_type" value="sanger" />
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
102 <param name="options_type_selector" value="basic" />
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
103 <output name="output_file" file="fastq_invalid-line3_fixed" />
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
104 </test>
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
105 <!-- Test fix-id by setting the option -->
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
106 <test>
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
107 <param name="input_file" value="fastq_invalid-line3" ftype="fastq" />
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
108 <param name="input_type" value="sanger" />
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
109 <param name="options_type_selector" value="advanced" />
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
110 <param name="fix_id" value="--fix-id" />
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
111 <output name="output_file" file="fastq_invalid-line3_fixed" />
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
112 </test>
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
113 <!-- Test fix-id / option not set; expect failure -->
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
114 <test expect_failure="true">
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
115 <param name="input_file" value="fastq_invalid-line3" ftype="fastq" />
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
116 <param name="input_type" value="sanger" />
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
117 <param name="options_type_selector" value="advanced" />
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
118 <param name="fix_id" value="--no-fix-id" />
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
119 </test>
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
120 <!-- 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
121 <!-- 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
122 <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
123 <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
124 <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
125 <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
126 <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
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 <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
129 <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
130 <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
131 <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
132 <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
133 </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
134 <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
135 <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
136 <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
137 <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
138 <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
139 </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
140 <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
141 <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
142 <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
143 <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
144 <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
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 <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
147 <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
148 <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
149 <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
150 <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
151 </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
152 <!-- 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
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 <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
155 <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
156 <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
157 <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
158 <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
159 <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
160 <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
161 </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
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 <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
164 <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
165 <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
166 <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
167 <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
168 <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
169 <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
170 </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
171 <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
172 <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
173 <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
174 <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
175 <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
176 <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
177 <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
178 <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
179 </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
180 <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
181 <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
182 <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
183 <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
184 <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
185 <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
186 <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
187 <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
188 </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
189 <!-- 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
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 <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
192 <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
193 <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
194 <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
195 <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
196 <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
197 <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
198 </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
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 <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
201 <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
202 <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
203 <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
204 <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
205 <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
206 <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
207 </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
208 <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
209 <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
210 <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
211 <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
212 <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
213 <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
214 <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
215 <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
216 </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
217 <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
218 <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
219 <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
220 <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
221 <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
222 <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
223 <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
224 <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
225 </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
226 <!-- 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
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 <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
229 <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
230 <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
231 <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
232 <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
233 <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
234 <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
235 </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
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 <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
238 <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
239 <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
240 <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
241 <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
242 <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
243 <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
244 </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
245 <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
246 <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
247 <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
248 <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
249 <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
250 <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
251 <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
252 <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
253 </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
254 <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
255 <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
256 <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
257 <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
258 <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
259 <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
260 <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
261 <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
262 </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
263 <!-- 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
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 <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
266 <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
267 <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
268 <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
269 <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
270 <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
271 <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
272 </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
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 <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
275 <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
276 <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
277 <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
278 <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
279 <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
280 <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
281 </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
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 <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
284 <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
285 <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
286 <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
287 <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
288 <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
289 <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
290 </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
291 <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
292 <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
293 <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
294 <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
295 <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
296 <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
297 <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
298 <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
299 </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
300 <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
301 <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
302 <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
303 <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
304 <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
305 <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
306 <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
307 <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
308 </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
309 <!-- 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
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 <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
312 <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
313 <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
314 <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
315 <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
316 <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
317 <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
318 </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
319 <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
320 <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
321 <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
322 <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
323 <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
324 <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
325 <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
326 <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
327 </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
328 <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
329 <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
330 <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
331 <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
332 <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
333 <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
334 <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
335 <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
336 </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
337 <!-- 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
338 <!-- 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
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 <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
341 <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
342 <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
343 <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
344 <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
345 <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
346 <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
347 </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
348 <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
349 <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
350 <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
351 <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
352 <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
353 <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
354 <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
355 <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
356 </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
357 <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
358 <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
359 <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
360 <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
361 <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
362 <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
363 <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
364 <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
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 <!-- 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
367 <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
368 <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
369 <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
370 <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
371 <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
372 <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
373 <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
374 <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
375 </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
376 <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
377 <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
378 <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
379 <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
380 <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
381 <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
382 <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
383 <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
384 </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
385 <!-- 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
386 <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
387 <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
388 <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
389 <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
390 <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
391 </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
392 <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
393 <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
394 <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
395 <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
396 <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
397 </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
398 </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
399 <help><![CDATA[
0
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
400 **What it does**
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
401
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
402 This tool offers several conversions options relating to the FASTQ format.
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
403
5
4fda2184efa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
404 When using *Basic* options, the output will be *sanger* formatted or *cssanger* formatted (when the input is Color Space Sanger). Inconsistent identifiers are fixed by default.
0
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
405
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
406 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
407
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
408 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
409
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
410 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
411
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
412 -----
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
413
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
414 **Quality Score Comparison**
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
415
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
416 ::
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
417
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
418 SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
419 ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
420 ..........................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
421 !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
0
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
422 | | | | | |
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
423 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
424
0
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
425 S - Sanger Phred+33, 93 values (0, 93) (0 to 60 expected in raw reads)
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
426 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
427 X - Solexa Solexa+64, 67 values (-5, 62) (-5 to 40 expected in raw reads)
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
428
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
429 Diagram adapted from http://en.wikipedia.org/wiki/FASTQ_format
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
430
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
431 .. class:: infomark
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
432
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
433 Output from Illumina 1.8+ pipelines are Sanger encoded.
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
434
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
435 ------
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
436
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
437 .. _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
438 ]]></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
439 <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
440 <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
441 </citations>
0
06c42572d7c0 Imported from capsule None
devteam
parents:
diff changeset
442 </tool>