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planemo upload for repository https://github.com/open2c/pairtools commit f60e7663dc3fd1a564e691ef35d35f35b0a851ad
author iuc
date Wed, 24 Sep 2025 11:49:16 +0000
parents 19f062c42798
children
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19f062c42798 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
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1 <tool id="pairtools_sort" name="Pairtools sort" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE_VERSION@" license="MIT">
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2 <description>Sort a 4dn pairs/pairsam file</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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19f062c42798 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'):
19f062c42798 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
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9 #set $input_link = "input.gz"
19f062c42798 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
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10 #set $output_sorted_pairs_link = "sorted_output.gz"
19f062c42798 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
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11 #else
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12 #set $input_link = "input"
19f062c42798 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
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13 #set $output_sorted_pairs_link = "sorted_output"
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14 #end if
19f062c42798 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
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15 ln -s '$pairs_path' '$input_link' &&
19f062c42798 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
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16 ln -s '$output_sorted_pairs' '$output_sorted_pairs_link' &&
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e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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17 pairtools sort
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19f062c42798 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
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18 '$input_link'
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19 -o '$output_sorted_pairs_link'
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20 --nproc-in \${GALAXY_SLOTS:-4}
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21 --nproc-out \${GALAXY_SLOTS:-4}
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22 ]]></command>
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23 <inputs>
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24 <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam,4dn_pairs.gz,4dn_pairsam.gz" label="Input file" help="Input a 4dn pairs or pairsam file"/>
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25 </inputs>
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26 <outputs>
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27 <data name="output_sorted_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}">
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28 </data>
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29 </outputs>
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30 <tests>
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31 <!--Test default parameters with pairs file, this us actually a pairsam file-->
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32 <test expect_num_outputs="1">
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33 <param name="pairs_path" ftype="4dn_pairsam" value="output_parsed_pairs_bam.pairs"/>
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34 <output name="output_sorted_pairs" file="output_sorted_pairs.pairs" ftype="4dn_pairsam" lines_diff="10"/>
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35 </test>
e90acf67d632 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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36 <!--Test default parameters with pairsam file-->
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37 <test expect_num_outputs="1">
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38 <param name="pairs_path" ftype="4dn_pairsam" value="output_dedup_pairs_markdups.pairsam"/>
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39 <output name="output_sorted_pairs" file="output_dedup_sorted.pairsam" ftype="4dn_pairsam" lines_diff="10"/>
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40 </test>
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41 <!--Test default parameters with pairsam file compressed output-->
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42 <test expect_num_outputs="1">
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43 <param name="pairs_path" ftype="4dn_pairsam" value="output_dedup_pairs_markdups.pairsam"/>
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44 <output name="output_sorted_pairs" file="output_dedup_sorted.pairsam" ftype="4dn_pairsam" decompress="true" lines_diff="10"/>
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45 </test>
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46 <!--Test default parameters with pairsam file compressed input-->
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47 <test expect_num_outputs="1">
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48 <param name="pairs_path" ftype="4dn_pairsam" value="output_dedup_pairs_markdups.pairsam.gz"/>
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49 <output name="output_sorted_pairs" file="output_dedup_sorted.pairsam" ftype="4dn_pairsam" lines_diff="10"/>
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50 </test>
0
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51 </tests>
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52 <help><![CDATA[
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53 **Pairtools sort**
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54
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55 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.
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57 ]]></help>
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58 <expand macro="citations"/>
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59 <expand macro="creator"/>
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60 </tool>