Mercurial > repos > devteam > tabular_to_fastq

annotate tabular_to_fastq.xml @ 4:2dcfbbf9071a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
author iuc
date Wed, 19 Feb 2020 12:59:28 -0500
parents 68f57cc8fad0
children 78fb18899c99
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
2dcfbbf9071a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 3
diff changeset
1 <tool id="tabular_to_fastq" name="Tabular to FASTQ" version="@TOOL_VERSION@">
2
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
2 <description>converter</description>
3
68f57cc8fad0 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 2
diff changeset
3 <edam_topics>
68f57cc8fad0 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 2
diff changeset
4 <edam_topic>topic_0622</edam_topic>
68f57cc8fad0 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 2
diff changeset
5 </edam_topics>
68f57cc8fad0 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 2
diff changeset
6 <edam_operations>
68f57cc8fad0 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 2
diff changeset
7 <edam_operation>operation_3434</edam_operation>
68f57cc8fad0 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 2
diff changeset
8 </edam_operations>
4
2dcfbbf9071a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 3
diff changeset
9 <macros>
2dcfbbf9071a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 3
diff changeset
10 <import>macros.xml</import>
2dcfbbf9071a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 3
diff changeset
11 </macros>
2dcfbbf9071a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 3
diff changeset
12 <requirements>
2dcfbbf9071a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 3
diff changeset
13 <requirement type="package" version="3.7">python</requirement>
2dcfbbf9071a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 3
diff changeset
14 </requirements>
2
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
15 <command><![CDATA[
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
16 python '$__tool_directory__/tabular_to_fastq.py' '$input_file' '$output_file' '$identifier' '$sequence' '$quality'
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
17 ]]></command>
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
18 <inputs>
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
19 <param name="input_file" type="data" format="tabular" label="Tabular file to convert" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
20 <param name="identifier" type="data_column" data_ref="input_file" label="Identifier column" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
21 <param name="sequence" type="data_column" data_ref="input_file" label="Sequence column" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
22 <param name="quality" type="data_column" data_ref="input_file" label="Quality column" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
23 </inputs>
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
24 <outputs>
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
25 <data name="output_file" format="fastq" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
26 </outputs>
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
27 <tests>
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
28 <!-- basic test -->
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
29 <test>
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
30 <param name="input_file" value="fastq_to_tabular_out_1.tabular" ftype="tabular" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
31 <param name="identifier" value="1" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
32 <param name="sequence" value="2" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
33 <param name="quality" value="3" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
34 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
35 </test>
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
36 <!-- color space test -->
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
37 <test>
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
38 <param name="input_file" value="fastq_to_tabular_out_2.tabular" ftype="tabular" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
39 <param name="identifier" value="1" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
40 <param name="sequence" value="2" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
41 <param name="quality" value="3" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
42 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
43 </test>
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
44 </tests>
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
45 <help><![CDATA[
0
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
46 **What it does**
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
47
2
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
48 This tool attempts to convert a tabular file containing sequencing read data to a FASTQ formatted file. The FASTQ Groomer tool should always be used on the output of this tool.
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
49 ]]></help>
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
50 <citations>
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
51 <citation type="doi">10.1093/bioinformatics/btq281</citation>
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
52 </citations>
0
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
53 </tool>