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comparison dedup.xml @ 8:914533f3507e draft

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planemo upload for repository https://github.com/open2c/pairtools commit d80cc18cb4f1f67065ed77c6225ef9cea906b727
author iuc
date Fri, 27 Jun 2025 20:33:05 +0000
parents 55a53b5e308d
children 41faa653d86c
comparison
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7:c162f3c43442 8:914533f3507e
13 #end if 13 #end if
14 $mark_dups 14 $mark_dups
15 #if $output_stats: 15 #if $output_stats:
16 --output-stats '$dedup_pairs_stats' 16 --output-stats '$dedup_pairs_stats'
17 #end if 17 #end if
18 #if $output_bytile_stats:
19 --keep-parent-id
20 --output-bytile-stats '$dedup_bytile_stats'
21 #end if
18 --nproc-in \${GALAXY_SLOTS:-4} 22 --nproc-in \${GALAXY_SLOTS:-4}
19 --nproc-out \${GALAXY_SLOTS:-4} 23 --nproc-out \${GALAXY_SLOTS:-4}
24 --max-mismatch ${max_mismatch}
20 ]]></command> 25 ]]></command>
21 <inputs> 26 <inputs>
22 <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam" label="Input pairs file" help="Input triu-flipped sorted .pairs or .pairsam file"/> 27 <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam" label="Input pairs file" help="Input triu-flipped sorted .pairs or .pairsam file"/>
23 <param argument="--mark-dups" type="boolean" truevalue="--mark-dups" falsevalue="" checked="True" label="Duplicate pairs are marked as DD in pair_type and as a duplicate in the SAM entries"/> 28 <param argument="--mark-dups" type="boolean" truevalue="--mark-dups" falsevalue="" checked="True" label="Duplicate pairs are marked as DD in pair_type and as a duplicate in the SAM entries"/>
24 <param argument="--output-dups" type="boolean" truevalue="--output-dups" falsevalue="" checked="False" label="Output file for duplicate pairs"/> 29 <param argument="--output-dups" type="boolean" truevalue="--output-dups" falsevalue="" checked="False" label="Output file for duplicate pairs"/>
25 <param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Output file for duplicate statistics"/> 30 <param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Output file for duplicate statistics"/>
31 <param argument="--max-mismatch" type="integer" value="3" min="0" label="Maximum number of mismatches. Pairs with both sides mapped within this distance &quot;bp&quot; from each other are considered duplicates."/>
32 <param argument="--output-bytile-stats" type="boolean" truevalue="--output-bytile-stats" falsevalue="" checked="False" label="Output file for optical duplicate statistics for datasets with original Illumina-generated read IDs."/>
26 </inputs> 33 </inputs>
27 <outputs> 34 <outputs>
28 <data name="output_dedup_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Deduplicated Pairs"/> 35 <data name="output_dedup_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Deduplicated Pairs"/>
29 <data name="output_dups_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Duplicate Pairs"> 36 <data name="output_dups_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Duplicate Pairs">
30 <filter>output_dups</filter> 37 <filter>output_dups</filter>
31 </data> 38 </data>
32 <data name="dedup_pairs_stats" format="tabular" label="${tool.name} on ${on_string}: Deduplicated stats"> 39 <data name="dedup_pairs_stats" format="tabular" label="${tool.name} on ${on_string}: Deduplicated stats">
33 <filter>output_stats</filter> 40 <filter>output_stats</filter>
34 </data> 41 </data>
42 <data name="dedup_bytile_stats" format="tabular" label="${tool.name} on ${on_string}: By-tile stats">
43 <filter>output_bytile_stats</filter>
44 </data>
35 </outputs> 45 </outputs>
36 <tests> 46 <tests>
47
37 <!--Test 01 with default parameters--> 48 <!--Test 01 with default parameters-->
38 <test expect_num_outputs="1"> 49 <test expect_num_outputs="1">
39 <param name="pairs_path" value="output_sorted_pairs.pairsam"/> 50 <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
40 <output name="output_dedup_pairs" file="output_dedup_pairs.pairsam" lines_diff="20"/> 51 <output name="output_dedup_pairs" file="output_dedup_pairs.pairsam" lines_diff="20"/>
41 </test> 52 </test>
53 <param name="mark_dups" value="true"></param> 64 <param name="mark_dups" value="true"></param>
54 <param name="output_stats" value="true"></param> 65 <param name="output_stats" value="true"></param>
55 <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" lines_diff="20"/> 66 <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"/> 67 <output name="dedup_pairs_stats" file="output_dedup_pairs.stats" lines_diff="20"/>
57 </test> 68 </test>
69 <!--Test 04 mark_dups and output_stats enabled, max_mismatch set to 0-->
70 <test expect_num_outputs="2">
71 <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
72 <param name="mark_dups" value="true"></param>
73 <param name="output_stats" value="true"></param>
74 <param name="max_mismatch" value="0"></param>
75 <output name="output_dedup_pairs" file="output_dedup_max_mismatch0_sorted.pairsam" lines_diff="20"/>
76 <output name="dedup_pairs_stats" file="output_dedup_max_mismatch0_sorted.stats" lines_diff="20"/>
77 </test>
78 <!--Test 05 mark_dups and output_stats + bytile_stats enabled-->
79 <test expect_num_outputs="3">
80 <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
81 <param name="mark_dups" value="true"></param>
82 <param name="output_stats" value="true"></param>
83 <param name="output_bytile_stats" value="true"></param>
84 <output name="output_dedup_pairs" file="output_dedup_max_parent_id_bytile_sorted.pairsam" lines_diff="20"/>
85 <output name="dedup_pairs_stats" file="output_dedup_max_parent_id_bytile_sorted.stats" lines_diff="20"/>
86 <output name="dedup_bytile_stats" file="output_dedup_max_parent_id_bytile_sorted_tile_dups.stats" lines_diff="20"/>
87 </test>
58 </tests> 88 </tests>
59 <help><![CDATA[ 89 <help><![CDATA[
60 **Pairtools dedup** 90 **Pairtools dedup**
61 91
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. 92 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.