Mercurial > repos > iuc > pairtools_split
changeset 9:7a125af14644 draft default tip
planemo upload for repository https://github.com/open2c/pairtools commit 5997d890c2a3fedff3c66d858cb1629b28138dc0
| author | iuc |
|---|---|
| date | Wed, 13 Aug 2025 20:06:03 +0000 |
| parents | 0fb51c6f2e37 |
| children | |
| files | macros.xml split.xml test-data/output_dedup_pairs_markdups.pairsam.gz test-data/output_parsed_pairs_sam.pairs.gz test-data/output_parsed_pairs_sam_assemblyname.pairs.gz test-data/output_sorted_pairs.pairsam.gz test-data/pairs_output2.stats.gz |
| diffstat | 7 files changed, 24 insertions(+), 8 deletions(-) [+] |
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--- a/macros.xml Fri Jul 25 13:54:22 2025 +0000 +++ b/macros.xml Wed Aug 13 20:06:03 2025 +0000 @@ -1,6 +1,7 @@ <macros> <token name="@TOOL_VERSION@">1.1.3</token> - <token name="@SUFFIX_VERSION@">1</token> + <token name="@SUFFIX_VERSION@">3</token> + <token name="@PROFILE_VERSION@">25.0</token> <xml name="edam_ontology"> <edam_datas> <edam_data>topic_1381</edam_data> @@ -29,4 +30,4 @@ <option value="3unique">3unique - Report the 3'-most unique alignment on each side, if present</option> <option value="all">all - Report all available unique alignments on each side</option> </xml> -</macros> \ No newline at end of file +</macros>
--- a/split.xml Fri Jul 25 13:54:22 2025 +0000 +++ b/split.xml Wed Aug 13 20:06:03 2025 +0000 @@ -1,29 +1,44 @@ -<tool id="pairtools_split" name="Pairtools split" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT"> +<tool id="pairtools_split" name="Pairtools split" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE_VERSION@" license="MIT"> <description>Split a pairsam file into pairs and SAM/BAM</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ + #if $pairsam_path.is_of_type('4dn_pairsam.gz'): + #set $input_link = "input.gz" + #set $output_pairs_link = "output_pairs.gz" + #else + #set $input_link = "input" + #set $output_pairs_link = "output_pairs" + #end if + ln -s '$pairsam_path' '$input_link' && + ln -s '$output_pairs' '$output_pairs_link' && pairtools split - '$pairsam_path' - --output-pairs '$output_pairs' + '$input_link' + --output-pairs '$output_pairs_link' --output-sam ./output.bam --nproc-in \${GALAXY_SLOTS:-4} --nproc-out \${GALAXY_SLOTS:-4} ]]></command> <inputs> - <param name="pairsam_path" type="data" format="4dn_pairsam" label="Input 4dn pairsam file"/> + <param name="pairsam_path" type="data" format="4dn_pairsam,4dn_pairsam.gz" label="Input 4dn pairsam file"/> </inputs> <outputs> - <data name="output_pairs" format="4dn_pairs" label="${tool.name} on ${on_string}: Output Pairs" /> + <data name="output_pairs" label="${tool.name} on ${on_string}: Output Pairs" auto_format="true" /> <data name="output_file" format="qname_sorted.bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}: Output BAM" /> </outputs> <tests> <!--Test default parameters--> <test expect_num_outputs="2"> <param name="pairsam_path" value="output_dedup_pairs_markdups.pairsam"/> - <output name="output_pairs" ftype="4dn_pairs" file="output_pairs_split.pairs" lines_diff="10"/> + <output name="output_pairs" file="output_pairs_split.pairs" ftype="4dn_pairs" lines_diff="10"/> + <output name="output_file" ftype="qname_sorted.bam" file="output_pairs_split.bam" lines_diff="20"/> + </test> + <!--Test default parameters and compressed input and output--> + <test expect_num_outputs="2"> + <param name="pairsam_path" value="output_dedup_pairs_markdups.pairsam.gz"/> + <output name="output_pairs" file="output_pairs_split.pairs" ftype="4dn_pairs.gz" decompress="true" lines_diff="10"/> <output name="output_file" ftype="qname_sorted.bam" file="output_pairs_split.bam" lines_diff="20"/> </test> </tests>