Mercurial > repos > rhpvorderman > fast_fastq_filter

annotate fast_fastq_filter.xml @ 0:5f0d949db99e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
author rhpvorderman
date Tue, 28 Dec 2021 14:17:40 +0000
parents
children 6ee24ca51829
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
1 <tool id="fast_fastq_filter" name="fastq-filter" version="0.1.0" python_template_version="3.5" profile="16.04">
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
2 <description>filter FASTQ reads fast</description>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
3 <requirements>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
4 <requirement type="package" version="0.1.0">fastq-filter</requirement>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
5 <!-- TODO: Remove this once biocontainer is published -->
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
6 <container type="docker">quay.io/rhpvorderman/fastq-filter:0.1.0</container>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
7 </requirements>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
9 #set all_filters = [str(filter['filter']) + ":" + str(filter['filter_threshold']) for filter in $filters]
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
10 fastq-filter -o '$output1'
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
11 #echo "'" + "|".join($all_filters) + "'"
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
12 '$input1'
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
13 ]]></command>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
14 <inputs>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
15 <param type="data" name="input1" label="Input FASTQ file" format="fastqsanger,fastqsanger.gz" />
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
16 <repeat name="filters" title="Filter" min="1">
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
17 <param name="filter" type="select" label="Filter on">
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
18 <option value="min_length">minimum length</option>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
19 <option value="max_length">maximum length</option>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
20 <option value="mean_quality" selected="true">mean quality</option>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
21 <option value="median_quality">median quality</option>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
22 </param>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
23 <param name="filter_threshold" type="integer" label="Filter threshold" value="20"/>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
24 </repeat>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
25 </inputs>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
26 <outputs>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
27 <!--Fastqsanger format for now. For conditionally applying fastqsanger.gz the tool needs
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
28 to be updated. An option is using format auto_detect, so we do not have to conditionally set
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
29 fastqsanger or fastqsanger.gz-->
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
30 <data name="output1" format="fastqsanger" />
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
31 <!--When the tool is updated for paired input, the optional paired output can probably be
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
32 found in the cutadapt wrapper -->
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
33 </outputs>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
34 <tests>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
35 <test>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
36 <param name="input1" value="input.fastq.gz"/>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
37 <output name="output1" file="output.fastq.gz"/>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
38 </test>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
39 </tests>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
40 <help><![CDATA[
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
41 The following filters are available:
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
42
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
43 + mean_quality:<quality> The mean quality of the FASTQ record is equal or above the given quality value.
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
44 + median_quality:<quality> The median quality of the FASTQ record is equal or above the given quality value.
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
45 + min_length:<length> The length of the sequence in the FASTQ record is at least min_length
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
46 + max_length:<length> The length of the sequence in the FASTQ record is at most max_length
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
47
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
48 ]]></help>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
49 <citations>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
50 <citation type="bibtex">
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
51 @misc{githubfastq-filter,
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
52 author = {Vorderman, Ruben Harmen Paul},
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
53 year = {2021},
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
54 title = {fastq-filter},
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
55 publisher = {GitHub},
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
56 journal = {GitHub repository},
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
57 url = {https://github.com/LUMC/fastq-filter},
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
58 }</citation>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
59 </citations>
5f0d949db99e "planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
rhpvorderman
parents:
diff changeset
60 </tool>