Mercurial > repos > iuc > seqwish

annotate seqwish.xml @ 0:7f7a074326ac 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/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
author iuc
date Wed, 08 Apr 2020 11:23:40 -0400
parents
children 189ae8d7e08e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
1 <tool id="seqwish" name="seqwish" version="@TOOL_VERSION@" >
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
2 <description>Alignment to variation graph inducer</description>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
3 <macros>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
4 <token name="@TOOL_VERSION@">0.4</token>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
5 </macros>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
6 <requirements>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
7 <requirement type="package" version="@TOOL_VERSION@">seqwish</requirement>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
8 </requirements>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
10 seqwish
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
11 -p '$paf_alns'
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
12 -s ${ ' '.join(["'%s'" % x for x in $seqs]) }
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
13 --gfa='$out_gfa'
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
14 #if $m:
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
15 -m '$m'
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
16 #end if
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
17 --threads=\${GALAXY_SLOTS:-1}
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
18 #if str($r):
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
19 -r $r
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
20 #end if
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
21 #if str($k):
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
22 -k $k
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
23 #end if
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
24 #if str($B):
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
25 -B $B
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
26 #end if
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
27 ]]></command>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
28 <inputs>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
29 <param argument="--paf-alns" type="data" format="paf" label="Induce the graph from these PAF formatted alignments" />
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
30 <param argument="--seqs" type="data" format="fasta,fasta.gz,fastq,fastq.gz" multiple="true" label="The sequences used to generate the alignments" />
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
31 <param argument="-m" type="data" optional="true" format="txt,tabular" label="Subset the input alignments"
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
32 help="" />
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
33 <param argument="-r" type="integer" min="1" optional="true" label="Limit copies of a given input base"
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
34 help="Limit transitive closure to include no more than N copies of a given input base" />
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
35 <param argument="-k" type="integer" min="1" optional="true" label="Filter exact matches below this length"
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
36 help="This can smooth the graph locally and prevent the formation of complex local graph topologies from forming due to differential alignments." />
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
37 <param argument="-B" type="integer" min="1" optional="true" label="Number of bp to use for transitive closure batch"
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
38 help="" />
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
39 </inputs>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
40
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
41 <outputs>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
42 <data name="out_gfa" format="gfa1" label="${tool.name} on ${on_string}" />
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
43 </outputs>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
44
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
45 <tests>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
46 <test>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
47 <param name="seqs" value="A-3105.fa.gz" />
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
48 <param name="paf_alns" value="A-3105.paf.gz" />
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
49 <output name="out_gfa" md5="176f9b4be76a2e69550da9b9c39ac5eb" />
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
50 </test>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
51 <test>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
52 <param name="seqs" value="A-3105.fa.gz" />
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
53 <param name="paf_alns" value="A-3105.paf.gz" />
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
54 <param name="r" value="3000" />
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
55 <param name="k" value="1" />
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
56 <param name="B" value="1000000" />
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
57 <output name="out_gfa" md5="176f9b4be76a2e69550da9b9c39ac5eb" />
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
58 </test>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
59 </tests>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
60 <help><![CDATA[
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
61 These **seq**uences **wish** they were squished into a graph.
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
62
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
63 seqwish implements a lossless conversion from pairwise alignments between sequences to a variation graph encoding the sequences
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
64 and their alignments. As input we typically take all-versus-all alignments, but the exact structure of the alignment set may
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
65 be defined in an application specific way. This algorithm uses a series of disk-backed sorts and passes over the alignment
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
66 and sequence inputs to allow the graph to be constructed from very large inputs that are commonly encountered when working with
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
67 large numbers of noisy input sequences. Memory usage during construction and traversal is limited by the use of sorted
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
68 disk-backed arrays and succinct rank/select dictionaries to record a queryable version of the graph.
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
69 ]]></help>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
70 <citations>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
71 </citations>
7f7a074326ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ commit eff85ef0f4297e12deda88b534627b231e218bde"
iuc
parents:
diff changeset
72 </tool>