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comparison dedup.xml @ 2:74df4a44471b draft

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planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
author iuc
date Thu, 18 Sep 2025 05:56:33 +0000
parents c99b93043a7f
children e36bce668b44
comparison
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1:054230c3643d 2:74df4a44471b
1 <tool id="pairtools_dedup" name="Pairtools dedup" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT"> 1 <tool id="pairtools_dedup" name="Pairtools dedup" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE_VERSION@" license="MIT">
2 <description>Find and remove PCR/optical duplicates</description> 2 <description>Find and remove PCR/optical duplicates</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #if $pairs_path.is_of_type('4dn_pairs.gz') or $pairs_path.is_of_type('4dn_pairsam.gz'):
9 #set $input_link = "input.gz"
10 #set $output_dedup_pairs_link = "output_dedup_pairs.ga"
11 #set $output_dups_pairs_link = "output_dups_pairs.gz"
12 #else
13 #set $input_link = "input"
14 #set $output_dedup_pairs_link = "output_dedup_pairs"
15 #set $output_dups_pairs_link = "output_dups_pairs"
16 #end if
17 ln -s '$pairs_path' '$input_link' &&
18 ln -s '$output_dedup_pairs' '$output_dedup_pairs_link' &&
19 ln -s '$output_dups_pairs' '$output_dups_pairs_link' &&
8 pairtools dedup 20 pairtools dedup
9 '$pairs_path' 21 '$input_link'
10 -o '$output_dedup_pairs' 22 -o '$output_dedup_pairs_link'
11 #if $output_dups: 23 #if $output_dups:
12 --output-dups '$output_dups_pairs' 24 --output-dups '$output_dups_pairs_link'
13 #end if 25 #end if
14 $mark_dups 26 $mark_dups
15 #if $output_stats: 27 #if $output_stats:
16 --output-stats '$dedup_pairs_stats' 28 --output-stats '$dedup_pairs_stats'
17 #end if 29 #end if
30 #if $output_bytile_stats:
31 --keep-parent-id
32 --output-bytile-stats '$dedup_bytile_stats'
33 #end if
18 --nproc-in \${GALAXY_SLOTS:-4} 34 --nproc-in \${GALAXY_SLOTS:-4}
19 --nproc-out \${GALAXY_SLOTS:-4} 35 --nproc-out \${GALAXY_SLOTS:-4}
36 --max-mismatch ${max_mismatch}
20 ]]></command> 37 ]]></command>
21 <inputs> 38 <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"/> 39 <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam,4dn_pairs.gz,4dn_pairsam.gz" 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"/> 40 <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"/> 41 <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"/> 42 <param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Output file for duplicate statistics"/>
43 <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."/>
44 <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."/>
45 <param name="compress_output" type="boolean" truevalue=".gz" falsevalue="" checked="false" label="Compress output files" />
26 </inputs> 46 </inputs>
27 <outputs> 47 <outputs>
28 <data name="output_dedup_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Deduplicated Pairs"/> 48 <data name="output_dedup_pairs" label="${tool.name} on ${on_string}: Deduplicated Pairs" format_source="pairs_path" />
29 <data name="output_dups_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Duplicate Pairs"> 49 <data name="output_dups_pairs" label="${tool.name} on ${on_string}: Duplicate Pairs" format_source="pairs_path" >
30 <filter>output_dups</filter> 50 <filter>output_dups</filter>
31 </data> 51 </data>
32 <data name="dedup_pairs_stats" format="tabular" label="${tool.name} on ${on_string}: Deduplicated stats"> 52 <data name="dedup_pairs_stats" format="tabular" label="${tool.name} on ${on_string}: Deduplicated stats">
33 <filter>output_stats</filter> 53 <filter>output_stats</filter>
34 </data> 54 </data>
55 <data name="dedup_bytile_stats" format="tabular" label="${tool.name} on ${on_string}: By-tile stats">
56 <filter>output_bytile_stats</filter>
57 </data>
35 </outputs> 58 </outputs>
36 <tests> 59 <tests>
37 <!--Test 01 with default parameters--> 60 <!--Test 01 with default parameters-->
38 <test expect_num_outputs="1"> 61 <test expect_num_outputs="1">
39 <param name="pairs_path" value="output_sorted_pairs.pairsam"/> 62 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>
40 <output name="output_dedup_pairs" file="output_dedup_pairs.pairsam" lines_diff="20"/> 63 <output name="output_dedup_pairs" file="output_dedup_pairs.pairsam" ftype="4dn_pairsam" lines_diff="20" />
41 </test> 64 </test>
42 <!--Test 02 mark_dups enabled and output_dups--> 65 <!--Test 02 with default parameters and compressed output-->
66 <test expect_num_outputs="1">
67 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>
68 <param name="compress_output" value="true"/>
69 <output name="output_dedup_pairs" file="output_dedup_pairs.pairsam" ftype="4dn_pairsam" decompress="true" lines_diff="20"/>
70 </test>
71 <!--Test 03 with default parameters and compressed iput-->
72 <test expect_num_outputs="1">
73 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam.gz"/>
74 <output name="output_dedup_pairs" file="output_dedup_pairs.pairsam" ftype="4dn_pairsam" lines_diff="20"/>
75 </test>
76 <!--Test 04 mark_dups enabled and output_dups-->
43 <test expect_num_outputs="2"> 77 <test expect_num_outputs="2">
44 <param name="pairs_path" value="output_sorted_pairs.pairsam"/> 78 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>
45 <param name="mark_dups" value="true"></param> 79 <param name="mark_dups" value="true"></param>
46 <param name="output_dups" value="true"></param> 80 <param name="output_dups" value="true"></param>
47 <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" lines_diff="20"/> 81 <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" ftype="4dn_pairsam" lines_diff="20"/>
48 <output name="output_dups_pairs" file="output_dups_pairs_markdups.pairsam" lines_diff="20"/> 82 <output name="output_dups_pairs" file="output_dups_pairs_markdups.pairsam" ftype="4dn_pairsam" lines_diff="20"/>
49 </test> 83 </test>
50 <!--Test 03 mark_dups and output_stats enabled--> 84 <!--Test 05 mark_dups and output_stats enabled-->
51 <test expect_num_outputs="2"> 85 <test expect_num_outputs="2">
52 <param name="pairs_path" value="output_sorted_pairs.pairsam"/> 86 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>
53 <param name="mark_dups" value="true"></param> 87 <param name="mark_dups" value="true"></param>
54 <param name="output_stats" value="true"></param> 88 <param name="output_stats" value="true"></param>
55 <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" lines_diff="20"/> 89 <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" ftype="4dn_pairsam" lines_diff="20"/>
56 <output name="dedup_pairs_stats" file="output_dedup_pairs.stats" lines_diff="20"/> 90 <output name="dedup_pairs_stats" file="output_dedup_pairs.stats" ftype="tabular" lines_diff="20"/>
91 </test>
92 <!--Test 06 mark_dups and output_stats enabled, max_mismatch set to 0-->
93 <test expect_num_outputs="2">
94 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>
95 <param name="mark_dups" value="true"></param>
96 <param name="output_stats" value="true"></param>
97 <param name="max_mismatch" value="0"></param>
98 <output name="output_dedup_pairs" file="output_dedup_max_mismatch0_sorted.pairsam" ftype="4dn_pairsam" lines_diff="20"/>
99 <output name="dedup_pairs_stats" file="output_dedup_max_mismatch0_sorted.stats" ftype="tabular" lines_diff="20"/>
100 </test>
101 <!--Test 07 mark_dups and output_stats + bytile_stats enabled-->
102 <test expect_num_outputs="3">
103 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>
104 <param name="mark_dups" value="true"></param>
105 <param name="output_stats" value="true"></param>
106 <param name="output_bytile_stats" value="true"></param>
107 <output name="output_dedup_pairs" file="output_dedup_max_parent_id_bytile_sorted.pairsam" ftype="4dn_pairsam" lines_diff="20"/>
108 <output name="dedup_pairs_stats" file="output_dedup_max_parent_id_bytile_sorted.stats" ftype="tabular" lines_diff="20"/>
109 <output name="dedup_bytile_stats" file="output_dedup_max_parent_id_bytile_sorted_tile_dups.stats" ftype="tabular" lines_diff="20"/>
110 </test>
111 <!--Test 08 mark_dups and output_stats + bytile_stats enabled, compress output-->
112 <test expect_num_outputs="3">
113 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>
114 <param name="mark_dups" value="true"></param>
115 <param name="output_stats" value="true"></param>
116 <param name="compress_output" value="true"></param>
117 <param name="output_bytile_stats" value="true"></param>
118 <output name="output_dedup_pairs" file="output_dedup_max_parent_id_bytile_sorted.pairsam" ftype="4dn_pairsam" decompress="true" lines_diff="20"/>
119 <output name="dedup_pairs_stats" file="output_dedup_max_parent_id_bytile_sorted.stats" ftype="tabular" decompress="true" lines_diff="20"/>
120 <output name="dedup_bytile_stats" file="output_dedup_max_parent_id_bytile_sorted_tile_dups.stats" ftype="tabular" decompress="true" lines_diff="20"/>
57 </test> 121 </test>
58 </tests> 122 </tests>
59 <help><![CDATA[ 123 <help><![CDATA[
60 **Pairtools dedup** 124 **Pairtools dedup**
61 125