Mercurial > repos > iuc > pairtools_sort
changeset 11:880d2519963f draft
planemo upload for repository https://github.com/open2c/pairtools commit 5997d890c2a3fedff3c66d858cb1629b28138dc0
| author | iuc |
|---|---|
| date | Wed, 13 Aug 2025 20:05:45 +0000 |
| parents | c1c1d894dd3a |
| children | ceeb94f87ba6 |
| files | macros.xml sort.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, 31 insertions(+), 12 deletions(-) [+] |
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--- a/macros.xml Fri Jul 25 13:55:10 2025 +0000 +++ b/macros.xml Wed Aug 13 20:05:45 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/sort.xml Fri Jul 25 13:55:10 2025 +0000 +++ b/sort.xml Wed Aug 13 20:05:45 2025 +0000 @@ -1,35 +1,53 @@ -<tool id="pairtools_sort" name="Pairtools sort" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT"> +<tool id="pairtools_sort" name="Pairtools sort" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE_VERSION@" license="MIT"> <description>Sort a 4dn pairs/pairsam file</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ + #if $pairs_path.is_of_type('4dn_pairs.gz') or $pairs_path.is_of_type('4dn_pairsam.gz'): + #set $input_link = "input.gz" + #set $output_sorted_pairs_link = "sorted_output.gz" + #else + #set $input_link = "input" + #set $output_sorted_pairs_link = "sorted_output" + #end if + ln -s '$pairs_path' '$input_link' && + ln -s '$output_sorted_pairs' '$output_sorted_pairs_link' && pairtools sort - '$pairs_path' - -o '$output_sorted_pairs' + '$input_link' + -o '$output_sorted_pairs_link' --nproc-in \${GALAXY_SLOTS:-4} --nproc-out \${GALAXY_SLOTS:-4} ]]></command> <inputs> - <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam" label="Input file" help="Input a 4dn pairs or pairsam file"/> + <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam,4dn_pairs.gz,4dn_pairsam.gz" label="Input file" help="Input a 4dn pairs or pairsam file"/> </inputs> <outputs> <data name="output_sorted_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}"> </data> </outputs> <tests> - <!--Test default parameters with pairs file--> + <!--Test default parameters with pairs file, this us actually a pairsam file--> <test expect_num_outputs="1"> - <param name="pairs_path" value="output_parsed_pairs_bam.pairs"/> - <output name="output_sorted_pairs" file="output_sorted_pairs.pairs" lines_diff="10"/> + <param name="pairs_path" ftype="4dn_pairsam" value="output_parsed_pairs_bam.pairs"/> + <output name="output_sorted_pairs" file="output_sorted_pairs.pairs" ftype="4dn_pairsam" lines_diff="10"/> </test> <!--Test default parameters with pairsam file--> <test expect_num_outputs="1"> - <param name="pairs_path" value="output_dedup_pairs_markdups.pairsam"/> - <output name="output_sorted_pairs" file="output_dedup_sorted.pairsam" lines_diff="10"/> + <param name="pairs_path" ftype="4dn_pairsam" value="output_dedup_pairs_markdups.pairsam"/> + <output name="output_sorted_pairs" file="output_dedup_sorted.pairsam" ftype="4dn_pairsam" lines_diff="10"/> </test> - + <!--Test default parameters with pairsam file compressed output--> + <test expect_num_outputs="1"> + <param name="pairs_path" ftype="4dn_pairsam" value="output_dedup_pairs_markdups.pairsam"/> + <output name="output_sorted_pairs" file="output_dedup_sorted.pairsam" ftype="4dn_pairsam" decompress="true" lines_diff="10"/> + </test> + <!--Test default parameters with pairsam file compressed input--> + <test expect_num_outputs="1"> + <param name="pairs_path" ftype="4dn_pairsam" value="output_dedup_pairs_markdups.pairsam.gz"/> + <output name="output_sorted_pairs" file="output_dedup_sorted.pairsam" ftype="4dn_pairsam" lines_diff="10"/> + </test> </tests> <help><![CDATA[ **Pairtools sort**