Mercurial > repos > iuc > pairtools_sort
diff sort.xml @ 2:19f062c42798 draft
planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
| author | iuc |
|---|---|
| date | Thu, 18 Sep 2025 05:57:12 +0000 |
| parents | e90acf67d632 |
| children |
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--- a/sort.xml Mon Mar 10 09:35:00 2025 +0000 +++ b/sort.xml Thu Sep 18 05:57:12 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**