annotate fastq_trim_poly_at.xml @ 1:ebca4912eabe 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
date Tue, 15 Feb 2022 16:38:32 +0000
parents dcc82e999439
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
1 <tool id="fastq_trim_poly_at" name="FASTQ poly-A|T trimmer" profile="18.01" version="0.25.1+galaxy0">
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
2 <description>Trims poly-A stretches at the 3'-end and poly-T at 5'-end of each read, optionally discarding reads with a length below the given threshold.</description>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
3 <requirements>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
4 <requirement type="package" version="0.25.1">fastq_utils</requirement>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
5 </requirements>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
7 fastq_trim_poly_at --file '$file' --outfile '$outfile'
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
8
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
9 #if '$min_poly_at_len':
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
10 --min_poly_at_len '$min_poly_at_len'
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
11 #end if
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
12
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
13 #if '$min_len':
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
14 --min_len '$min_len'
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
15 #end if
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
16 ]]></command>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
17 <inputs>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
18 <param name="file" label="Input file" argument="--file" type="data" format="fastqsanger.gz" optional="false" help="Fastq (optional gzipped) file name"/>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
19 <param name="min_poly_at_len" label="Minimum Poly-AT Length" argument="--min_poly_at_len" optional="true" type="integer" min="0" help="Minimum length of poly-A|T sequence to remove"/>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
20 <param name="min_len" label="Minimum Quality" optional="true" value="" argument="--min_qual" type="integer" help="Minimum read length"/>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
21 </inputs>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
22 <outputs>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
23 <data label="${tool.name} on ${on_string}: Output file" name="outfile" format="fastqsanger.gz" />
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
24 </outputs>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
25 <tests>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
26 <test>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
27 <param name="file" value="poly_at.fastq.gz"/>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
28 <param name="min_poly_at_len" value="3"/>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
29 <output name="outfile" file="poly_at_len3.fastq.gz" compare="sim_size" delta_frac="0.1"/>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
30 </test>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
31 </tests>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
32 <help><![CDATA[
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
33 =======================================================
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
34 FASTQ poly-A|T trimmer (fastq_trim_poly_at)
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
35 =======================================================
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
36
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
37 Minimum Poly-AT Length - The terminal poly-A|T sequence
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
38 should be at least this long to be removed
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
39
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
40 Minimum Length - Reads with post-trimming length less
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
41 than this setting will be removed
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
42
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
43 ]]></help>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
44 <citations>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
45 <citation type="bibtex"><![CDATA[
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
46 @ARTICLE{Fonseca2017,
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
47 author = {Fonseca, N.},
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
48 title = {fastq_utils},
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
49 year = {2017},
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
50 publisher = {GitHub},
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
51 journal = {GitHub repository},
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
52 howpublished = {\url{https://github.com/nunofonseca/fastq_utils}},
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
53 commit = {c6cf3f954c5286e62fbe36bb9ffecd89d7823b07}
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
54 }]]></citation>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
55 </citations>
dcc82e999439 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
ebi-gxa
parents:
diff changeset
56 </tool>