Mercurial > repos > iuc > ivar_filtervariants

annotate ivar_filtervariants.xml @ 20:161e04f498db 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/ivar/ commit 97f230215d53e71748c78cd21633d92143710b94
author iuc
date Wed, 06 Aug 2025 08:22:40 +0000
parents d328d99d7396
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
8f8df367470d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 02d1d482bda9804c69d2d03c890151bc491e5c73
iuc
parents: 11
diff changeset
1 <tool id="ivar_filtervariants" name="ivar filtervariants" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
0
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
2 <description>Filter variants across replicates or multiple samples aligned using the same reference</description>
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
3 <macros>
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
5 </macros>
18
d328d99d7396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit b548a504e88bd330f534be0dd018175c9341b1f1
iuc
parents: 12
diff changeset
6 <expand macro="xrefs"/>
11
72ddd32392cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents: 0
diff changeset
7 <expand macro="requirements"/>
72ddd32392cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents: 0
diff changeset
8 <expand macro="version_command"/>
0
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
10 #for $counter, $input in enumerate($inputs):
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
11 ln -s '$input' ./var_${counter}.tsv &&
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
12 #end for
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
13 ivar filtervariants
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
14 -p filtered.tsv
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
15 #for $counter, $input in enumerate($inputs)
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
16 ./var_${counter}.tsv
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
17 #end for
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
18 ]]></command>
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
19 <inputs>
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
20 <param name="inputs" type="data" format="tabular" multiple="true" label="Variant tsv files for each replicate"/>
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
21 </inputs>
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
22 <outputs>
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
23 <data name="output_filtered" format="tabular" label="${tool.name} on ${on_string}" from_work_dir="filtered.tsv"/>
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
24 </outputs>
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
25 <tests>
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
26 <test>
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
27 <param name="inputs" value="zika/Z52_a.tsv,zika/Z52_b.tsv" ftype="tabular"/>
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
28 <output name="output_filtered" file="zika/Z52.tsv" ftype="tabular" lines_diff="10"/>
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
29 </test>
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
30 </tests>
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
31 <help><![CDATA[
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
32 iVar can be used to get an intersection of variants(in .tsv files) called
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
33 from any number of replicates or from different samples using the same
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
34 reference sequence. This intersection will filter out any iSNVs that do not
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
35 occur in a minimum fraction of the files supplied. This parameter can be
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
36 changed using the -t flag which range from 0 to 1 (default). Fields that are
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
37 different across replicates(fields apart from REGION, POS, REF, ALT,
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
38 REF_CODON, REF_AA, ALT_CODON, ALT_AA) will have the filename added as a
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
39 suffix. If there are a large number of files to be filtered, the -f flag can
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
40 be used to supply a text file with one sample/replicate variant .tsv file
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
41 per line.
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
42
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
43 Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
44 ]]></help>
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
45 <expand macro="citations" />
c88553ec696e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
46 </tool>