Mercurial > repos > iuc > pairtools_sort

annotate sort.xml @ 0:e90acf67d632 draft

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planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
author iuc
date Sun, 22 Dec 2024 15:40:15 +0000
parents
children 19f062c42798
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e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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1 <tool id="pairtools_sort" name="Pairtools sort" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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2 <description>Sort a 4dn pairs/pairsam file</description>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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3 <macros>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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4 <import>macros.xml</import>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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5 </macros>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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6 <expand macro="requirements"/>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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7 <command detect_errors="exit_code"><![CDATA[
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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8 pairtools sort
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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9 '$pairs_path'
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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10 -o '$output_sorted_pairs'
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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11 --nproc-in \${GALAXY_SLOTS:-4}
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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12 --nproc-out \${GALAXY_SLOTS:-4}
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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13 ]]></command>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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14 <inputs>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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15 <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam" label="Input file" help="Input a 4dn pairs or pairsam file"/>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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16 </inputs>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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17 <outputs>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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18 <data name="output_sorted_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}">
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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19 </data>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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20 </outputs>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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21 <tests>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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22 <!--Test default parameters with pairs file-->
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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23 <test expect_num_outputs="1">
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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24 <param name="pairs_path" value="output_parsed_pairs_bam.pairs"/>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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25 <output name="output_sorted_pairs" file="output_sorted_pairs.pairs" lines_diff="10"/>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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26 </test>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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27 <!--Test default parameters with pairsam file-->
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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28 <test expect_num_outputs="1">
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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29 <param name="pairs_path" value="output_dedup_pairs_markdups.pairsam"/>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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30 <output name="output_sorted_pairs" file="output_dedup_sorted.pairsam" lines_diff="10"/>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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31 </test>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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32
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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33 </tests>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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34 <help><![CDATA[
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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35 **Pairtools sort**
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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36
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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37 Sort pairs in the lexicographic order along chrom1 and chrom2, in the numeric order along pos1 and pos2 and in the lexicographic order along pair_type.
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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38
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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39 ]]></help>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
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40 <expand macro="citations"/>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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41 <expand macro="creator"/>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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42 </tool>