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annotate dedup.xml @ 0:c99b93043a7f draft

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planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
author iuc
date Sun, 22 Dec 2024 15:39:43 +0000
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children 74df4a44471b
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c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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1 <tool id="pairtools_dedup" name="Pairtools dedup" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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2 <description>Find and remove PCR/optical duplicates</description>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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3 <macros>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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4 <import>macros.xml</import>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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5 </macros>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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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[
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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8 pairtools dedup
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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9 '$pairs_path'
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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10 -o '$output_dedup_pairs'
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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11 #if $output_dups:
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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12 --output-dups '$output_dups_pairs'
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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13 #end if
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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14 $mark_dups
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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15 #if $output_stats:
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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16 --output-stats '$dedup_pairs_stats'
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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17 #end if
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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18 --nproc-in \${GALAXY_SLOTS:-4}
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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19 --nproc-out \${GALAXY_SLOTS:-4}
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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20 ]]></command>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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21 <inputs>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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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"/>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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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"/>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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24 <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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25 <param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Output file for duplicate statistics"/>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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26 </inputs>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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27 <outputs>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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28 <data name="output_dedup_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Deduplicated Pairs"/>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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29 <data name="output_dups_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Duplicate Pairs">
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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30 <filter>output_dups</filter>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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31 </data>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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32 <data name="dedup_pairs_stats" format="tabular" label="${tool.name} on ${on_string}: Deduplicated stats">
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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33 <filter>output_stats</filter>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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34 </data>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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35 </outputs>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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36 <tests>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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37 <!--Test 01 with default parameters-->
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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38 <test expect_num_outputs="1">
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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39 <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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40 <output name="output_dedup_pairs" file="output_dedup_pairs.pairsam" lines_diff="20"/>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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41 </test>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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42 <!--Test 02 mark_dups enabled and output_dups-->
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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43 <test expect_num_outputs="2">
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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44 <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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45 <param name="mark_dups" value="true"></param>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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46 <param name="output_dups" value="true"></param>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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47 <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" lines_diff="20"/>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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48 <output name="output_dups_pairs" file="output_dups_pairs_markdups.pairsam" lines_diff="20"/>
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49 </test>
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50 <!--Test 03 mark_dups and output_stats enabled-->
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51 <test expect_num_outputs="2">
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52 <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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53 <param name="mark_dups" value="true"></param>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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54 <param name="output_stats" value="true"></param>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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55 <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" lines_diff="20"/>
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56 <output name="dedup_pairs_stats" file="output_dedup_pairs.stats" lines_diff="20"/>
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57 </test>
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58 </tests>
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59 <help><![CDATA[
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60 **Pairtools dedup**
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61
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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.
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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63
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64 ]]></help>
c99b93043a7f planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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65 <expand macro="citations"/>
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66 <expand macro="creator"/>
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67 </tool>