Mercurial > repos > bgruening > graphmap_align

annotate graphmap_align.xml @ 1:1c6c961851de 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/bgruening/galaxytools/tree/master/tools/graphmap commit ba787e88cb93e78516b2fced5b60285d5f033ca3
author bgruening
date Fri, 15 Mar 2024 13:12:50 +0000
parents 190175f4e143
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
1 <tool id="graphmap_align" name="Mapper" version="@VERSION@">
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
2 <description>for long, error-prone reads, like Nanopore ONT and PacBio</description>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
3 <macros>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
4 <import>macros.xml</import>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
5 </macros>
1
1c6c961851de planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit ba787e88cb93e78516b2fced5b60285d5f033ca3
bgruening
parents: 0
diff changeset
6 <expand macro="xrefs" />
0
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
7 <expand macro="requirements" />
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
8 <command detect_errors="exit_code">
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
9 <![CDATA[
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
10 ln -s '$r' ref.${r.ext} &&
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
11 ln -s '$d' reads.${d.ext} &&
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
12
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
13 graphmap align
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
14 -r ref.${r.ext}
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
15 -d reads.${d.ext}
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
16 #if $preset:
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
17 -x $preset
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
18 #end if
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
19 -t \${GALAXY_SLOTS:-4} |
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
20 samtools view -b -u | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o output.bam -
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
21 ]]></command>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
22 <inputs>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
23 <param argument="-r" type="data" format="fasta,fastq" label="reference sequence" />
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
24 <param argument="-d" type="data" format="fasta,fastq" label="reads" />
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
25 <param name="preset" type="select" optional="True" label="Pre-set parameters to increase sensitivity for different sequencing technologies. (-x)">
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
26 <option value="illumina">illumina preset</option>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
27 <option value="overlap">overlap preset</option>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
28 <option value="sensitive">sensitive preset</option>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
29 </param>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
30 <!--
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
31 <param type="data" name="reference" format="fasta,fastq" label="Sequences"/>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
32 <param type="data" name="reads" format="fasta,fastq" label="Sequences"/>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
33 <param type="data" name="overlaps" format="sam,tabular" label="Overlaps"/>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
34 <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences"/> -->
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
35
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
36 </inputs>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
37 <outputs>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
38 <data name="output" format="bam" from_work_dir="output.bam" />
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
39 </outputs>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
40 <tests>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
41 <test>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
42 <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
43 <param name="d" value="E.coli_contigs.fasta"/>
1
1c6c961851de planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit ba787e88cb93e78516b2fced5b60285d5f033ca3
bgruening
parents: 0
diff changeset
44 <output name="output" ftype="bam" file="result1_map.bam" lines_diff="2"/>
0
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
45 </test>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
46 <test>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
47 <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
48 <param name="d" value="E.coli_contigs.fasta"/>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
49 <param name="preset" value="illumina"/>
1
1c6c961851de planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit ba787e88cb93e78516b2fced5b60285d5f033ca3
bgruening
parents: 0
diff changeset
50 <output name="output" ftype="bam" file="result2_map.bam" lines_diff="2"/>
0
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
51 </test>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
52 <test>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
53 <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
54 <param name="d" value="E.coli_contigs.fasta"/>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
55 <param name="preset" value="sensitive"/>
1
1c6c961851de planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit ba787e88cb93e78516b2fced5b60285d5f033ca3
bgruening
parents: 0
diff changeset
56 <output name="output" ftype="bam" file="result3_map.bam" lines_diff="2"/>
0
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
57 </test></tests>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
58 <help><![CDATA[
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
59 GraphMap - A very accurate and sensitive long-read, high error-rate sequence mapper
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
60 GraphMap (c) by Ivan Sovic, Mile Sikic and Niranjan Nagarajan
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
61 GraphMap is licensed under The MIT License.
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
62 ]]></help>
190175f4e143 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
bgruening
parents:
diff changeset
63 <expand macro="citations" />
1
1c6c961851de planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit ba787e88cb93e78516b2fced5b60285d5f033ca3
bgruening
parents: 0
diff changeset
64 </tool>