Mercurial > repos > iuc > khmer_filter_abundance

annotate filter-abund.xml @ 7:8c6433857aa8 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/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
author iuc
date Wed, 18 Dec 2019 16:05:31 -0500
parents 03246d4ea8cd
children 97f65399e30d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
8c6433857aa8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 1
diff changeset
1 <tool id="khmer_filter_abundance" name="khmer: Filter reads" version="@WRAPPER_VERSION@@TOOL_VERSION@">
0
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
2 <description>
1
03246d4ea8cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents: 0
diff changeset
3 by minimal k-mer abundance
0
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
4 </description>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
5 <macros>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
6 <token name="@BINARY@">filter-abund.py</token>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
7 <import>macros.xml</import>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
8 </macros>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
9 <expand macro="requirements" />
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
10 <expand macro="stdio" />
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
11 <expand macro="version" />
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
12 <command><![CDATA[
7
8c6433857aa8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 1
diff changeset
13 set -u &&
8c6433857aa8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 1
diff changeset
14 @LINK_SEQUENCES@
0
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
15 mkdir output && cd output &&
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
16 @BINARY@
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
17 --cutoff=${cutoff}
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
18 ${variable_coverage}
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
19 @THREADS@
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
20 ${input_countgraph_filename}
7
8c6433857aa8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 1
diff changeset
21 @USE_SEQUENCES@
0
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
22 ]]>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
23 </command>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
24 <inputs>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
25 <expand macro="input_sequences_filenames" />
7
8c6433857aa8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 1
diff changeset
26 <param argument="--variable_coverage" name="variable_coverage" type="boolean" checked="false" truevalue="--variable-coverage" falsevalue=""
0
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
27 label="Variable coverage"
7
8c6433857aa8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 1
diff changeset
28 help="Only trim when a sequence has high enough coverage; median abundance > 20" />
8c6433857aa8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 1
diff changeset
29 <param argument="--cutoff" name="cutoff" type="integer" value="2" label="Cutoff"
8c6433857aa8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 1
diff changeset
30 help="Trim at k-mers below this abundance" />
0
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
31 <expand macro="input_countgraph_filename" />
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
32 </inputs>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
33 <outputs>
7
8c6433857aa8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 1
diff changeset
34 <expand macro="output_sequences" extension="abundfilt"/>
0
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
35 </outputs>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
36 <tests>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
37 <test>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
38 <param name="inputs" value="test-abund-read-2.fa" />
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
39 <param name="input_countgraph_filename"
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
40 value="test-abund-read-2.oxlicg" ftype="oxlicg" />
7
8c6433857aa8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 1
diff changeset
41 <output_collection name="sequences" type="list">
8c6433857aa8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 1
diff changeset
42 <element name="test-abund-read-2.fa">
0
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
43 <assert_contents>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
44 <has_text text="GGTTGACGGGGCTCAGGG" />
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
45 </assert_contents>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
46 </element>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
47 </output_collection>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
48 </test>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
49 <test>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
50 <param name="inputs" value="test-abund-read-2.fa" />
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
51 <param name="input_countgraph_filename"
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
52 value="test-abund-read-2.oxlicg" ftype="oxlicg" />
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
53 <param name="cutoff" value="1" />
7
8c6433857aa8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 1
diff changeset
54 <output_collection name="sequences" type="list">
8c6433857aa8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 1
diff changeset
55 <element name="test-abund-read-2.fa">
0
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
56 <assert_contents>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
57 <has_text text="GGTTGACGGGGCTCAGGG" />
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
58 </assert_contents>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
59 </element>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
60 </output_collection>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
61 </test>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
62 </tests>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
63 <help><![CDATA[
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
64 Trims fastq/fasta sequences at k-mers of a given abundance based on a provided k-mer countgraph
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
65
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
66 If the input sequences are from RNAseq or metagenome sequencing then
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
67 `--variable-coverage` should be used.
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
68
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
69 @HELP_FOOTER@
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
70 ]]>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
71 </help>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
72 <citations>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
73 <expand macro="software-citation" />
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
74 <expand macro="counting-citation" />
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
75 </citations>
71f98f6f68af planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
76 </tool>