Mercurial > repos > iuc > pairtools_dedup

annotate dedup.xml @ 9:608ea80cccba draft

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planemo upload for repository https://github.com/open2c/pairtools commit 365c6f6387b2f90af22a62e673873b90e7f7394a
author iuc
date Fri, 25 Jul 2025 13:54:54 +0000
parents 914533f3507e
children 41faa653d86c
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f8c1d2a93d43 planemo upload for repository https://github.com/open2c/pairtools commit e9ebcf7ac032fafaa445e654b245df679a4bbf18
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1 <tool id="pairtools_dedup" name="Pairtools dedup" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" 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"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 pairtools dedup
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9 '$pairs_path'
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10 -o '$output_dedup_pairs'
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11 #if $output_dups:
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12 --output-dups '$output_dups_pairs'
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13 #end if
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14 $mark_dups
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15 #if $output_stats:
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16 --output-stats '$dedup_pairs_stats'
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17 #end if
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18 #if $output_bytile_stats:
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19 --keep-parent-id
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20 --output-bytile-stats '$dedup_bytile_stats'
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21 #end if
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22 --nproc-in \${GALAXY_SLOTS:-4}
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23 --nproc-out \${GALAXY_SLOTS:-4}
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24 --max-mismatch ${max_mismatch}
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25 ]]></command>
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26 <inputs>
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27 <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam" label="Input pairs file" help="Input triu-flipped sorted .pairs or .pairsam file"/>
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28 <param argument="--mark-dups" type="boolean" truevalue="--mark-dups" falsevalue="" checked="True" label="Duplicate pairs are marked as DD in pair_type and as a duplicate in the SAM entries"/>
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29 <param argument="--output-dups" type="boolean" truevalue="--output-dups" falsevalue="" checked="False" label="Output file for duplicate pairs"/>
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30 <param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Output file for duplicate statistics"/>
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31 <param argument="--max-mismatch" type="integer" value="3" min="0" label="Maximum number of mismatches. Pairs with both sides mapped within this distance &quot;bp&quot; from each other are considered duplicates."/>
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32 <param argument="--output-bytile-stats" type="boolean" truevalue="--output-bytile-stats" falsevalue="" checked="False" label="Output file for optical duplicate statistics for datasets with original Illumina-generated read IDs."/>
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33 </inputs>
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34 <outputs>
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35 <data name="output_dedup_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Deduplicated Pairs"/>
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36 <data name="output_dups_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Duplicate Pairs">
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37 <filter>output_dups</filter>
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38 </data>
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39 <data name="dedup_pairs_stats" format="tabular" label="${tool.name} on ${on_string}: Deduplicated stats">
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40 <filter>output_stats</filter>
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41 </data>
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42 <data name="dedup_bytile_stats" format="tabular" label="${tool.name} on ${on_string}: By-tile stats">
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43 <filter>output_bytile_stats</filter>
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44 </data>
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45 </outputs>
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46 <tests>
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47
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48 <!--Test 01 with default parameters-->
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49 <test expect_num_outputs="1">
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50 <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
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51 <output name="output_dedup_pairs" file="output_dedup_pairs.pairsam" lines_diff="20"/>
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52 </test>
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53 <!--Test 02 mark_dups enabled and output_dups-->
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54 <test expect_num_outputs="2">
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55 <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
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56 <param name="mark_dups" value="true"></param>
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57 <param name="output_dups" value="true"></param>
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58 <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" lines_diff="20"/>
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59 <output name="output_dups_pairs" file="output_dups_pairs_markdups.pairsam" lines_diff="20"/>
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60 </test>
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61 <!--Test 03 mark_dups and output_stats enabled-->
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62 <test expect_num_outputs="2">
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63 <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
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64 <param name="mark_dups" value="true"></param>
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65 <param name="output_stats" value="true"></param>
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66 <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" lines_diff="20"/>
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67 <output name="dedup_pairs_stats" file="output_dedup_pairs.stats" lines_diff="20"/>
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68 </test>
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69 <!--Test 04 mark_dups and output_stats enabled, max_mismatch set to 0-->
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70 <test expect_num_outputs="2">
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71 <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
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72 <param name="mark_dups" value="true"></param>
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73 <param name="output_stats" value="true"></param>
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74 <param name="max_mismatch" value="0"></param>
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75 <output name="output_dedup_pairs" file="output_dedup_max_mismatch0_sorted.pairsam" lines_diff="20"/>
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76 <output name="dedup_pairs_stats" file="output_dedup_max_mismatch0_sorted.stats" lines_diff="20"/>
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77 </test>
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78 <!--Test 05 mark_dups and output_stats + bytile_stats enabled-->
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79 <test expect_num_outputs="3">
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80 <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
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81 <param name="mark_dups" value="true"></param>
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82 <param name="output_stats" value="true"></param>
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83 <param name="output_bytile_stats" value="true"></param>
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84 <output name="output_dedup_pairs" file="output_dedup_max_parent_id_bytile_sorted.pairsam" lines_diff="20"/>
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85 <output name="dedup_pairs_stats" file="output_dedup_max_parent_id_bytile_sorted.stats" lines_diff="20"/>
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86 <output name="dedup_bytile_stats" file="output_dedup_max_parent_id_bytile_sorted_tile_dups.stats" lines_diff="20"/>
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87 </test>
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88 </tests>
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89 <help><![CDATA[
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90 **Pairtools dedup**
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91
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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.
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93
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94 ]]></help>
f8c1d2a93d43 planemo upload for repository https://github.com/open2c/pairtools commit e9ebcf7ac032fafaa445e654b245df679a4bbf18
iuc
parents:
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95 <expand macro="citations"/>
f8c1d2a93d43 planemo upload for repository https://github.com/open2c/pairtools commit e9ebcf7ac032fafaa445e654b245df679a4bbf18
iuc
parents:
diff changeset
96 <expand macro="creator"/>
f8c1d2a93d43 planemo upload for repository https://github.com/open2c/pairtools commit e9ebcf7ac032fafaa445e654b245df679a4bbf18
iuc
parents:
diff changeset
97 </tool>