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annotate stats.xml @ 0:8d02c649a347 draft

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planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
author iuc
date Sun, 22 Dec 2024 15:40:00 +0000
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children 4c6af50296d0
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8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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1 <tool id="pairtools_stats" name="Pairtools Stats" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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2 <description>Calculates pairs statistics for input pairs and pairsam files.</description>
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3 <macros>
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4 <import>macros.xml</import>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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5 </macros>
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6 <expand macro="requirements"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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7 <command detect_errors="exit_code"><![CDATA[
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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8 pairtools stats
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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9 $merge
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10 $with_chromsizes
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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11 $yaml
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12 -o '$pairs_output'
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13 --nproc-in \${GALAXY_SLOTS:-4}
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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14 --nproc-out \${GALAXY_SLOTS:-4}
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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15 #if $input_file:
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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16 ${str($input_file).replace(',', ' ')}
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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17 #end if
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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18 ]]></command>
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19 <inputs>
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20 <param type="data" name="input_file" format="4dn_pairs,4dn_pairsam" multiple="true" label="Input pairs or pairsam file" help="Input 4dn pairs or pairsam file"></param>
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21 <param type="boolean" argument="--merge" truevalue="--merge" falsevalue="" checked="False" label="Merge input stats files" help="If selected, will merge multiple input stats files instead of calculating statistics of .pairs/.pairsam file"></param>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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22 <param type="boolean" argument="--with-chromsizes" truevalue="--with-chromsizes" falsevalue="" checked="False" label="Store sizes of chromosomes from the header of the pairs file in the stats file"></param>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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23 <param type="boolean" argument="--yaml" truevalue="--yaml" falsevalue="" checked="False" label="Output stats in yaml format instead of table"></param>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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24 </inputs>
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25 <outputs>
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26 <data name="pairs_output" format="tabular" label="${tool.name} on ${on_string}"/>
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27 </outputs>
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28 <tests>
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29 <!--Test 01 with pair file as input and default parameters-->
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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30 <test expect_num_outputs="1">
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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31 <param name="input_file" value="output_parsed_pairs_sam.pairs"/>
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32 <param name="merge" value="false"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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33 <param name="with_chromsizes" value="false"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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34 <param name="yaml" value="false"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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35 <output name="pairs_output" ftype="tabular" file="pairs_output.stats"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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36 </test>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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37 <!--Test 02 with multipe input pair files as input and default parameters-->
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38 <test expect_num_outputs="1">
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39 <param name="input_file" value="pairs_output.stats,pairs_output2.stats"/>
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40 <param name="merge" value="true"/>
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41 <param name="with_chromsizes" value="false"/>
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42 <param name="yaml" value="false"/>
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43 <output name="pairs_output" ftype="tabular" file="pairs_output_merged.stats" lines_diff="40"/>
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44 </test>
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45 <!--Test 03 with pair files as input with additional chromsizes in output-->
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46 <test expect_num_outputs="1">
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47 <param name="input_file" value="output_parsed_pairs_sam.pairs"/>
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48 <param name="merge" value="false"/>
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49 <param name="with_chromsizes" value="true"/>
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50 <param name="yaml" value="false"/>
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51 <output name="pairs_output" ftype="tabular" file="pairs_output_with_chromsize.stats"/>
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52 </test>
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53 <!--Test 04 with pair files as input and yaml output format-->
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54 <test expect_num_outputs="1">
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55 <param name="input_file" value="output_parsed_pairs_sam.pairs"/>
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56 <param name="merge" value="false"/>
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57 <param name="with_chromsizes" value="false"/>
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58 <param name="yaml" value="true"/>
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59 <output name="pairs_output" ftype="tabular" file="pairs_output_yaml.stats"/>
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63
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64 Calculate pairs statistics.
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65
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66 By default, uses 4dn pairs or 4dn pairsam file to calculate statistics.
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67
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68 ]]></help>
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69 <expand macro="citations"/>
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70 </tool>