Mercurial > repos > iuc > pairtools_dedup

annotate 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
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74df4a44471b planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
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1 <tool id="pairtools_dedup" name="Pairtools dedup" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE_VERSION@" license="MIT">
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2 <description>Find and remove PCR/optical duplicates</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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7 <command detect_errors="exit_code"><![CDATA[
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74df4a44471b planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
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8 #if $pairs_path.is_of_type('4dn_pairs.gz') or $pairs_path.is_of_type('4dn_pairsam.gz'):
74df4a44471b planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
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9 #set $input_link = "input.gz"
74df4a44471b planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
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10 #set $output_dedup_pairs_link = "output_dedup_pairs.ga"
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11 #set $output_dups_pairs_link = "output_dups_pairs.gz"
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12 #else
74df4a44471b planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
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13 #set $input_link = "input"
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14 #set $output_dedup_pairs_link = "output_dedup_pairs"
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15 #set $output_dups_pairs_link = "output_dups_pairs"
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16 #end if
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17 ln -s '$pairs_path' '$input_link' &&
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18 ln -s '$output_dedup_pairs' '$output_dedup_pairs_link' &&
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19 ln -s '$output_dups_pairs' '$output_dups_pairs_link' &&
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c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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20 pairtools dedup
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21 '$input_link'
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22 -o '$output_dedup_pairs_link'
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23 #if $output_dups:
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24 --output-dups '$output_dups_pairs_link'
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25 #end if
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26 $mark_dups
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27 #if $output_stats:
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28 --output-stats '$dedup_pairs_stats'
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29 #end if
2
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30 #if $output_bytile_stats:
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31 --keep-parent-id
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32 --output-bytile-stats '$dedup_bytile_stats'
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33 #end if
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34 --nproc-in \${GALAXY_SLOTS:-4}
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35 --nproc-out \${GALAXY_SLOTS:-4}
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36 --max-mismatch ${max_mismatch}
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37 ]]></command>
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38 <inputs>
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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"/>
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c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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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"/>
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41 <param argument="--output-dups" type="boolean" truevalue="--output-dups" falsevalue="" checked="False" label="Output file for duplicate pairs"/>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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42 <param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Output file for duplicate statistics"/>
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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."/>
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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."/>
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45 <param name="compress_output" type="boolean" truevalue=".gz" falsevalue="" checked="false" label="Compress output files" />
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46 </inputs>
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47 <outputs>
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48 <data name="output_dedup_pairs" label="${tool.name} on ${on_string}: Deduplicated Pairs" format_source="pairs_path" />
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49 <data name="output_dups_pairs" label="${tool.name} on ${on_string}: Duplicate Pairs" format_source="pairs_path" >
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50 <filter>output_dups</filter>
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51 </data>
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52 <data name="dedup_pairs_stats" format="tabular" label="${tool.name} on ${on_string}: Deduplicated stats">
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53 <filter>output_stats</filter>
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54 </data>
2
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55 <data name="dedup_bytile_stats" format="tabular" label="${tool.name} on ${on_string}: By-tile stats">
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56 <filter>output_bytile_stats</filter>
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57 </data>
0
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58 </outputs>
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59 <tests>
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60 <!--Test 01 with default parameters-->
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61 <test expect_num_outputs="1">
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62 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>
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63 <output name="output_dedup_pairs" file="output_dedup_pairs.pairsam" ftype="4dn_pairsam" lines_diff="20" />
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64 </test>
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65 <!--Test 02 with default parameters and compressed output-->
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66 <test expect_num_outputs="1">
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67 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>
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68 <param name="compress_output" value="true"/>
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69 <output name="output_dedup_pairs" file="output_dedup_pairs.pairsam" ftype="4dn_pairsam" decompress="true" lines_diff="20"/>
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70 </test>
2
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71 <!--Test 03 with default parameters and compressed iput-->
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72 <test expect_num_outputs="1">
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73 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam.gz"/>
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74 <output name="output_dedup_pairs" file="output_dedup_pairs.pairsam" ftype="4dn_pairsam" lines_diff="20"/>
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75 </test>
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76 <!--Test 04 mark_dups enabled and output_dups-->
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77 <test expect_num_outputs="2">
2
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78 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>
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79 <param name="mark_dups" value="true"></param>
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80 <param name="output_dups" value="true"></param>
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81 <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" ftype="4dn_pairsam" lines_diff="20"/>
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82 <output name="output_dups_pairs" file="output_dups_pairs_markdups.pairsam" ftype="4dn_pairsam" lines_diff="20"/>
0
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83 </test>
2
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84 <!--Test 05 mark_dups and output_stats enabled-->
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85 <test expect_num_outputs="2">
2
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86 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>
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87 <param name="mark_dups" value="true"></param>
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88 <param name="output_stats" value="true"></param>
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89 <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" ftype="4dn_pairsam" lines_diff="20"/>
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90 <output name="dedup_pairs_stats" file="output_dedup_pairs.stats" ftype="tabular" lines_diff="20"/>
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91 </test>
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92 <!--Test 06 mark_dups and output_stats enabled, max_mismatch set to 0-->
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93 <test expect_num_outputs="2">
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94 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>
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95 <param name="mark_dups" value="true"></param>
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96 <param name="output_stats" value="true"></param>
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97 <param name="max_mismatch" value="0"></param>
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98 <output name="output_dedup_pairs" file="output_dedup_max_mismatch0_sorted.pairsam" ftype="4dn_pairsam" lines_diff="20"/>
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99 <output name="dedup_pairs_stats" file="output_dedup_max_mismatch0_sorted.stats" ftype="tabular" lines_diff="20"/>
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100 </test>
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101 <!--Test 07 mark_dups and output_stats + bytile_stats enabled-->
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102 <test expect_num_outputs="3">
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103 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>
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104 <param name="mark_dups" value="true"></param>
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105 <param name="output_stats" value="true"></param>
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106 <param name="output_bytile_stats" value="true"></param>
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107 <output name="output_dedup_pairs" file="output_dedup_max_parent_id_bytile_sorted.pairsam" ftype="4dn_pairsam" lines_diff="20"/>
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108 <output name="dedup_pairs_stats" file="output_dedup_max_parent_id_bytile_sorted.stats" ftype="tabular" lines_diff="20"/>
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109 <output name="dedup_bytile_stats" file="output_dedup_max_parent_id_bytile_sorted_tile_dups.stats" ftype="tabular" lines_diff="20"/>
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110 </test>
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111 <!--Test 08 mark_dups and output_stats + bytile_stats enabled, compress output-->
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112 <test expect_num_outputs="3">
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113 <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>
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114 <param name="mark_dups" value="true"></param>
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115 <param name="output_stats" value="true"></param>
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116 <param name="compress_output" value="true"></param>
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117 <param name="output_bytile_stats" value="true"></param>
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118 <output name="output_dedup_pairs" file="output_dedup_max_parent_id_bytile_sorted.pairsam" ftype="4dn_pairsam" decompress="true" lines_diff="20"/>
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119 <output name="dedup_pairs_stats" file="output_dedup_max_parent_id_bytile_sorted.stats" ftype="tabular" decompress="true" lines_diff="20"/>
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120 <output name="dedup_bytile_stats" file="output_dedup_max_parent_id_bytile_sorted_tile_dups.stats" ftype="tabular" decompress="true" lines_diff="20"/>
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121 </test>
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122 </tests>
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123 <help><![CDATA[
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124 **Pairtools dedup**
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125
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126 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.
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127
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128 ]]></help>
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129 <expand macro="citations"/>
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130 <expand macro="creator"/>
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131 </tool>