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comparison dedup.xml @ 10:41faa653d86c draft

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planemo upload for repository https://github.com/open2c/pairtools commit 5997d890c2a3fedff3c66d858cb1629b28138dc0
author iuc
date Wed, 13 Aug 2025 20:05:12 +0000
parents 914533f3507e
children 3d1d241ceff2
comparison
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9:608ea80cccba 10:41faa653d86c
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
22 --nproc-in \${GALAXY_SLOTS:-4} 34 --nproc-in \${GALAXY_SLOTS:-4}
23 --nproc-out \${GALAXY_SLOTS:-4} 35 --nproc-out \${GALAXY_SLOTS:-4}
24 --max-mismatch ${max_mismatch} 36 --max-mismatch ${max_mismatch}
25 ]]></command> 37 ]]></command>
26 <inputs> 38 <inputs>
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"/> 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"/>
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"/> 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"/>
29 <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"/>
30 <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"/>
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."/> 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."/>
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."/> 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" />
33 </inputs> 46 </inputs>
34 <outputs> 47 <outputs>
35 <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 ${on_string}: Deduplicated Pairs" format_source="pairs_path" />
36 <data name="output_dups_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Duplicate Pairs"> 49 <data name="output_dups_pairs" label="${tool.name} on ${on_string}: Duplicate Pairs" format_source="pairs_path" >
37 <filter>output_dups</filter> 50 <filter>output_dups</filter>
38 </data> 51 </data>
39 <data name="dedup_pairs_stats" format="tabular" label="${tool.name} on ${on_string}: Deduplicated stats"> 52 <data name="dedup_pairs_stats" format="tabular" label="${tool.name} on ${on_string}: Deduplicated stats">
40 <filter>output_stats</filter> 53 <filter>output_stats</filter>
41 </data> 54 </data>
42 <data name="dedup_bytile_stats" format="tabular" label="${tool.name} on ${on_string}: By-tile stats"> 55 <data name="dedup_bytile_stats" format="tabular" label="${tool.name} on ${on_string}: By-tile stats">
43 <filter>output_bytile_stats</filter> 56 <filter>output_bytile_stats</filter>
44 </data> 57 </data>
45 </outputs> 58 </outputs>
46 <tests> 59 <tests>
47
48 <!--Test 01 with default parameters--> 60 <!--Test 01 with default parameters-->
49 <test expect_num_outputs="1"> 61 <test expect_num_outputs="1">
50 <param name="pairs_path" value="output_sorted_pairs.pairsam"/> 62 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>
51 <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" />
52 </test> 64 </test>
53 <!--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-->
54 <test expect_num_outputs="2"> 77 <test expect_num_outputs="2">
55 <param name="pairs_path" value="output_sorted_pairs.pairsam"/> 78 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>
56 <param name="mark_dups" value="true"></param> 79 <param name="mark_dups" value="true"></param>
57 <param name="output_dups" value="true"></param> 80 <param name="output_dups" value="true"></param>
58 <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"/>
59 <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"/>
60 </test> 83 </test>
61 <!--Test 03 mark_dups and output_stats enabled--> 84 <!--Test 05 mark_dups and output_stats enabled-->
62 <test expect_num_outputs="2"> 85 <test expect_num_outputs="2">
63 <param name="pairs_path" value="output_sorted_pairs.pairsam"/> 86 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>
64 <param name="mark_dups" value="true"></param> 87 <param name="mark_dups" value="true"></param>
65 <param name="output_stats" value="true"></param> 88 <param name="output_stats" value="true"></param>
66 <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"/>
67 <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"/>
68 </test> 91 </test>
69 <!--Test 04 mark_dups and output_stats enabled, max_mismatch set to 0--> 92 <!--Test 06 mark_dups and output_stats enabled, max_mismatch set to 0-->
70 <test expect_num_outputs="2"> 93 <test expect_num_outputs="2">
71 <param name="pairs_path" value="output_sorted_pairs.pairsam"/> 94 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>
72 <param name="mark_dups" value="true"></param> 95 <param name="mark_dups" value="true"></param>
73 <param name="output_stats" value="true"></param> 96 <param name="output_stats" value="true"></param>
74 <param name="max_mismatch" value="0"></param> 97 <param name="max_mismatch" value="0"></param>
75 <output name="output_dedup_pairs" file="output_dedup_max_mismatch0_sorted.pairsam" lines_diff="20"/> 98 <output name="output_dedup_pairs" file="output_dedup_max_mismatch0_sorted.pairsam" ftype="4dn_pairsam" lines_diff="20"/>
76 <output name="dedup_pairs_stats" file="output_dedup_max_mismatch0_sorted.stats" lines_diff="20"/> 99 <output name="dedup_pairs_stats" file="output_dedup_max_mismatch0_sorted.stats" ftype="tabular" lines_diff="20"/>
77 </test> 100 </test>
78 <!--Test 05 mark_dups and output_stats + bytile_stats enabled--> 101 <!--Test 07 mark_dups and output_stats + bytile_stats enabled-->
79 <test expect_num_outputs="3"> 102 <test expect_num_outputs="3">
80 <param name="pairs_path" value="output_sorted_pairs.pairsam"/> 103 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>
81 <param name="mark_dups" value="true"></param> 104 <param name="mark_dups" value="true"></param>
82 <param name="output_stats" value="true"></param> 105 <param name="output_stats" value="true"></param>
83 <param name="output_bytile_stats" value="true"></param> 106 <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"/> 107 <output name="output_dedup_pairs" file="output_dedup_max_parent_id_bytile_sorted.pairsam" ftype="4dn_pairsam" lines_diff="20"/>
85 <output name="dedup_pairs_stats" file="output_dedup_max_parent_id_bytile_sorted.stats" lines_diff="20"/> 108 <output name="dedup_pairs_stats" file="output_dedup_max_parent_id_bytile_sorted.stats" ftype="tabular" lines_diff="20"/>
86 <output name="dedup_bytile_stats" file="output_dedup_max_parent_id_bytile_sorted_tile_dups.stats" 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"/>
87 </test> 121 </test>
88 </tests> 122 </tests>
89 <help><![CDATA[ 123 <help><![CDATA[
90 **Pairtools dedup** 124 **Pairtools dedup**
91 125