Mercurial > repos > devteam > fastqtofasta

annotate fastq_to_fasta.xml @ 5:ac3fed111eb6 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/fastqtofasta commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
author iuc
date Fri, 04 Oct 2024 10:35:33 +0000
parents 297962e79f39
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
ac3fed111eb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
iuc
parents: 4
diff changeset
1 <tool id="fastq_to_fasta_python" name="FASTQ to FASTA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
2 <description>converter</description>
4
297962e79f39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 3
diff changeset
3 <macros>
297962e79f39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 3
diff changeset
4 <import>macros.xml</import>
297962e79f39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 3
diff changeset
5 </macros>
3
a64c24430f5e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 2
diff changeset
6 <edam_topics>
a64c24430f5e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 2
diff changeset
7 <edam_topic>topic_0622</edam_topic>
a64c24430f5e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 2
diff changeset
8 </edam_topics>
a64c24430f5e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 2
diff changeset
9 <edam_operations>
a64c24430f5e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 2
diff changeset
10 <edam_operation>operation_3434</edam_operation>
a64c24430f5e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 2
diff changeset
11 </edam_operations>
5
ac3fed111eb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
iuc
parents: 4
diff changeset
12 <expand macro="requirements"/>
2
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
13 <command><![CDATA[
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
14 gx-fastq-to-fasta '$input_file' '$output_file' '${input_file.extension[len('fastq'):]}'
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
15 ]]></command>
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
16 <inputs>
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
17 <param name="input_file" type="data" format="fastq,fastq.gz,fastq.bz2" label="FASTQ file to convert" />
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
18 </inputs>
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
19 <outputs>
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
20 <data name="output_file" format="fasta" />
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
21 </outputs>
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
22 <tests>
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
23 <!-- basic test -->
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
24 <test>
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
25 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
26 <output name="output_file" file="fastq_to_fasta_python_1.out" />
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
27 </test>
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
28 <!-- color space test -->
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
29 <test>
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
30 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
31 <output name="output_file" file="fastq_to_fasta_python_2.out" />
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
32 </test>
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
33 <!-- test of ignoring invalid score values: this input has ascii characters falling outside of illumina range, but they should not matter -->
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
34 <test>
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
35 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqillumina" />
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
36 <output name="output_file" file="fastq_to_fasta_python_1.out" />
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
37 </test>
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
38 </tests>
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
39 <help><![CDATA[
0
3571553aeb20 Imported from capsule None
devteam
parents:
diff changeset
40 **What it does**
3571553aeb20 Imported from capsule None
devteam
parents:
diff changeset
41
3571553aeb20 Imported from capsule None
devteam
parents:
diff changeset
42 This tool converts FASTQ sequencing reads to FASTA sequences.
2
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
43 ]]></help>
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
44 <citations>
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
45 <citation type="doi">10.1093/bioinformatics/btq281</citation>
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
46 </citations>
0
3571553aeb20 Imported from capsule None
devteam
parents:
diff changeset
47 </tool>