Mercurial > repos > iuc > khmer_extract_partitions

annotate extract-partitions.xml @ 11:43ffe9695c10 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/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
author iuc
date Thu, 03 Oct 2024 13:45:20 +0000
parents 13e404fd854b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
e245209affce "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 14ea2dc5ef36219c908ed64b256794711ce7b902"
iuc
parents: 8
diff changeset
1 <tool id="khmer_extract_partitions" name="khmer: Extract partitions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
2 <description>Separate sequences that are annotated with partitions into grouped files</description>
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
3 <macros>
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
4 <token name="@BINARY@">extract-partitions.py</token>
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
5 <import>macros.xml</import>
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
6 </macros>
11
43ffe9695c10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
7 <expand macro="bio_tools"/>
0
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
8 <expand macro="requirements" />
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
9 <expand macro="stdio" />
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
10 <expand macro="version" />
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
11 <command><![CDATA[
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
12 mkdir -p output &&
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
13 cd output &&
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
14 @BINARY@
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
15 --max-size $max_size
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
16 --min-partition-size $min_partition_size
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
17 $output_unassigned
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
18 output
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
19 #for input in $inputs
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
20 $input
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
21 #end for
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
22 ]]>
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
23 </command>
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
24 <inputs>
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
25 <expand macro="input_sequences_filenames" />
11
43ffe9695c10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
26 <param argument="--max-size" type="integer" label="Max group size" value="1000000"
8
f388b06c8f48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 0
diff changeset
27 help="No more than this many number of sequences will be stored in each output"/>
0
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
28 <param name="min_partition_size" type="integer" label="Min partition size" value="5"
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
29 help="The minimum partition size worth keeping (--min-partition-size/-m)" />
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
30 <param name="output_unassigned" type="boolean" checked="false" truevalue="--output-unassigned" falsevalue=""
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
31 label="Output unassigned sequences" help="(--output-unassigned/-U)" />
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
32 </inputs>
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
33 <outputs>
11
43ffe9695c10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
34 <data name="distribution" format="txt" from_work_dir="output/output.dist" label="${tool.name} on ${on_string}: Partition size distribution" />
43ffe9695c10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
35 <collection name="groups_of_partitions" type="list" format="fasta">
43ffe9695c10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
36 <discover_datasets pattern="__name__" directory="output" format="fasta"/>
0
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
37 </collection>
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
38 </outputs>
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
39 <tests>
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
40 <test>
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
41 <param name="inputs" value="random-20-a.fa.part"/>
11
43ffe9695c10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
42 <output name="distribution">
43ffe9695c10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
43 <assert_contents>
43ffe9695c10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
44 <has_text text="99 1 1 99"/>
43ffe9695c10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
45 </assert_contents>
43ffe9695c10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
46 </output>
43ffe9695c10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
47 <output_collection name="groups_of_partitions">
0
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
48 <element name="output.group0000.fa" file="random-20-a.part.extract.fa" />
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
49 </output_collection>
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
50 </test>
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
51
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
52 </tests>
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
53 <help><![CDATA[
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
54 Separate sequences that are annotated with partitions into grouped files.
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
55
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
56 @HELP_FOOTER@
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
57 ]]>
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
58 </help>
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
59 <citations>
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
60 <expand macro="software-citation" />
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
61 <expand macro="graph-citation" />
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
62 </citations>
78fa1a753c00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
63 </tool>