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comparison dedup.xml @ 0:c99b93043a7f draft

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planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
author iuc
date Sun, 22 Dec 2024 15:39:43 +0000
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children 74df4a44471b
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-1:000000000000 0:c99b93043a7f
1 <tool id="pairtools_dedup" name="Pairtools dedup" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
2 <description>Find and remove PCR/optical duplicates</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 pairtools dedup
9 '$pairs_path'
10 -o '$output_dedup_pairs'
11 #if $output_dups:
12 --output-dups '$output_dups_pairs'
13 #end if
14 $mark_dups
15 #if $output_stats:
16 --output-stats '$dedup_pairs_stats'
17 #end if
18 --nproc-in \${GALAXY_SLOTS:-4}
19 --nproc-out \${GALAXY_SLOTS:-4}
20 ]]></command>
21 <inputs>
22 <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam" label="Input pairs file" help="Input triu-flipped sorted .pairs or .pairsam file"/>
23 <param argument="--mark-dups" type="boolean" truevalue="--mark-dups" falsevalue="" checked="True" label="Duplicate pairs are marked as DD in pair_type and as a duplicate in the SAM entries"/>
24 <param argument="--output-dups" type="boolean" truevalue="--output-dups" falsevalue="" checked="False" label="Output file for duplicate pairs"/>
25 <param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Output file for duplicate statistics"/>
26 </inputs>
27 <outputs>
28 <data name="output_dedup_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Deduplicated Pairs"/>
29 <data name="output_dups_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Duplicate Pairs">
30 <filter>output_dups</filter>
31 </data>
32 <data name="dedup_pairs_stats" format="tabular" label="${tool.name} on ${on_string}: Deduplicated stats">
33 <filter>output_stats</filter>
34 </data>
35 </outputs>
36 <tests>
37 <!--Test 01 with default parameters-->
38 <test expect_num_outputs="1">
39 <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
40 <output name="output_dedup_pairs" file="output_dedup_pairs.pairsam" lines_diff="20"/>
41 </test>
42 <!--Test 02 mark_dups enabled and output_dups-->
43 <test expect_num_outputs="2">
44 <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
45 <param name="mark_dups" value="true"></param>
46 <param name="output_dups" value="true"></param>
47 <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" lines_diff="20"/>
48 <output name="output_dups_pairs" file="output_dups_pairs_markdups.pairsam" lines_diff="20"/>
49 </test>
50 <!--Test 03 mark_dups and output_stats enabled-->
51 <test expect_num_outputs="2">
52 <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
53 <param name="mark_dups" value="true"></param>
54 <param name="output_stats" value="true"></param>
55 <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" lines_diff="20"/>
56 <output name="dedup_pairs_stats" file="output_dedup_pairs.stats" lines_diff="20"/>
57 </test>
58 </tests>
59 <help><![CDATA[
60 **Pairtools dedup**
61
62 Find PCR/optical duplicates in an upper-triangular flipped sorted pairs/pairsam file. Allow for a +/-N bp mismatch at each side of duplicated molecules.
63
64 ]]></help>
65 <expand macro="citations"/>
66 <expand macro="creator"/>
67 </tool>