Mercurial > repos > ebi-gxa > fastq_filter_n
comparison fastq_filter_n.xml @ 0:df87d29fac7f draft default tip
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
author | ebi-gxa |
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date | Tue, 15 Feb 2022 16:38:56 +0000 |
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1 <tool id="fastq_filter_n" name="FASTQ filterer" profile="18.01" version="0.25.1+galaxy0"> | |
2 <description>Discards reads with more than x% of uncalled bases (N)</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.25.1">fastq_utils</requirement> | |
5 </requirements> | |
6 <command detect_errors="exit_code"><![CDATA[ | |
7 fastq_filter_n -n '$threshold' '$file' > $outfile | |
8 ]]></command> | |
9 <inputs> | |
10 <param name="file" label="Input file" type="data" format="fastqsanger.gz" optional="false" help="Fastq (optional gzipped) file name"/> | |
11 <param name="threshold" label="Filter threshold" argument="-n" optional="true" value="0" type="integer" min="0" max="100" help="[0-100] Maximum percentage of uncalled bases in a read. Default is 0."/> | |
12 </inputs> | |
13 <outputs> | |
14 <data label="${tool.name} on ${on_string}: Output file" name="outfile" format="fastqsanger.gz" /> | |
15 </outputs> | |
16 <tests> | |
17 <test> | |
18 <param name="file" value="test_21_2.fastq.gz"/> | |
19 <param name="threshold" value="5"/> | |
20 <output name="outfile" md5="019ce04559162b973e13a514a5c01595"/> | |
21 </test> | |
22 </tests> | |
23 <help><![CDATA[ | |
24 ============================================================ | |
25 FASTQ filterer (fastq_filter_n) | |
26 ============================================================ | |
27 | |
28 Outputs a gzipped fastq file where reads with more than the | |
29 maximum number of allowed uncalled bases are not included. | |
30 | |
31 Threshold is the maximum percentage (ranging from 0 to 100) | |
32 of uncalled bases that a read can have. Default value is 0, | |
33 which means that a read with a single N would be discarded. | |
34 | |
35 ]]></help> | |
36 <citations> | |
37 <citation type="bibtex"><![CDATA[ | |
38 @ARTICLE{Fonseca2017, | |
39 author = {Fonseca, N.}, | |
40 title = {fastq_utils}, | |
41 year = {2017}, | |
42 publisher = {GitHub}, | |
43 journal = {GitHub repository}, | |
44 howpublished = {\url{https://github.com/nunofonseca/fastq_utils}}, | |
45 commit = {c6cf3f954c5286e62fbe36bb9ffecd89d7823b07} | |
46 }]]></citation> | |
47 </citations> | |
48 </tool> |