Mercurial > repos > iuc > pairtools_stats

annotate stats.xml @ 3:0f660a127740 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/open2c/pairtools commit f60e7663dc3fd1a564e691ef35d35f35b0a851ad
author iuc
date Wed, 24 Sep 2025 11:49:36 +0000
parents 4c6af50296d0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
1 <tool id="pairtools_stats" name="Pairtools Stats" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE_VERSION@" license="MIT">
0
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
2 <description>Calculates pairs statistics for input pairs and pairsam files.</description>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
3 <macros>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
4 <import>macros.xml</import>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
5 </macros>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
2
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
8 #if $merge:
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
9 #set $input_file_links = str($input_file).replace(',', ' ')
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
10 #else
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
11 #set $input_file_links = ""
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
12 #for $i, $f in enumerate($input_file):
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
13 #if $f.is_of_type('4dn_pairs.gz') or $f.is_of_type('4dn_pairsam.gz'):
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
14 ln -s '$f' 'input_file_${i}.gz' &&
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
15 #set $input_file_links += ' input_file_%d.gz ' % $i
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
16 #else:
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
17 ln -s '$f' 'input_file_${i}' &&
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
18 #set $input_file_links += ' input_file_%d ' % $i
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
19 #end if
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
20 #end for
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
21 #end if
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
22
0
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
23 pairtools stats
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
24 $merge
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
25 $with_chromsizes
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
26 $yaml
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
27 -o '$pairs_output'
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
28 --nproc-in \${GALAXY_SLOTS:-4}
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
29 --nproc-out \${GALAXY_SLOTS:-4}
2
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
30 $input_file_links
0
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
31 ]]></command>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
32 <inputs>
2
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
33 <param type="data" name="input_file" format="4dn_pairs,4dn_pairsam,4dn_pairs.gz,4dn_pairsam.gz" multiple="true" label="Input pairs or pairsam file" help="Input 4dn pairs or pairsam file"></param>
0
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
34 <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
iuc
parents:
diff changeset
35 <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
iuc
parents:
diff changeset
36 <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
iuc
parents:
diff changeset
37 </inputs>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
38 <outputs>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
39 <data name="pairs_output" format="tabular" label="${tool.name} on ${on_string}"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
40 </outputs>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
41 <tests>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
42 <!--Test 01 with pair file as input and default parameters-->
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
43 <test expect_num_outputs="1">
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
44 <param name="input_file" value="output_parsed_pairs_sam.pairs"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
45 <param name="merge" value="false"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
46 <param name="with_chromsizes" value="false"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
47 <param name="yaml" value="false"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
48 <output name="pairs_output" ftype="tabular" file="pairs_output.stats"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
49 </test>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
50 <!--Test 02 with multipe input pair files as input and default parameters-->
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
51 <test expect_num_outputs="1">
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
52 <param name="input_file" value="pairs_output.stats,pairs_output2.stats"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
53 <param name="merge" value="true"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
54 <param name="with_chromsizes" value="false"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
55 <param name="yaml" value="false"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
56 <output name="pairs_output" ftype="tabular" file="pairs_output_merged.stats" lines_diff="40"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
57 </test>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
58 <!--Test 03 with pair files as input with additional chromsizes in output-->
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
59 <test expect_num_outputs="1">
2
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
60 <param name="input_file" ftype="4dn_pairs" value="output_parsed_pairs_sam.pairs"/>
0
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
61 <param name="merge" value="false"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
62 <param name="with_chromsizes" value="true"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
63 <param name="yaml" value="false"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
64 <output name="pairs_output" ftype="tabular" file="pairs_output_with_chromsize.stats"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
65 </test>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
66 <!--Test 04 with pair files as input and yaml output format-->
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
67 <test expect_num_outputs="1">
2
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
68 <param name="input_file" ftype="4dn_pairs" value="output_parsed_pairs_sam.pairs"/>
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
69 <param name="merge" value="false"/>
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
70 <param name="with_chromsizes" value="false"/>
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
71 <param name="yaml" value="true"/>
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
72 <output name="pairs_output" ftype="tabular" file="pairs_output_yaml.stats"/>
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
73 </test>
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
74 <!--Test 05 with compressed input pair file as input and default parameters-->
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
75 <test expect_num_outputs="1">
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
76 <param name="input_file" ftype="4dn_pairs" value="output_parsed_pairs_sam.pairs.gz"/>
0
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
77 <param name="merge" value="false"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
78 <param name="with_chromsizes" value="false"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
79 <param name="yaml" value="true"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
80 <output name="pairs_output" ftype="tabular" file="pairs_output_yaml.stats"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
81 </test>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
82 </tests>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
83 <help><![CDATA[
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
84
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
85 Calculate pairs statistics.
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
86
2
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
87 By default, uses 4dn pairs or 4dn pairsam file to calculate statistics. Setting merge to true will
4c6af50296d0 planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
iuc
parents: 0
diff changeset
88 merge multiple input stats files instead of calculating statistics of .pairs/.pairsam file.
0
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
89
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
90 ]]></help>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
91 <expand macro="citations"/>
8d02c649a347 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
iuc
parents:
diff changeset
92 </tool>