| Previous changeset 9:608ea80cccba (2025-07-25) Next changeset 11:7a2b37ae4a50 (2025-08-28) |
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Commit message:
planemo upload for repository https://github.com/open2c/pairtools commit 5997d890c2a3fedff3c66d858cb1629b28138dc0 |
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modified:
dedup.xml macros.xml |
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added:
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 |
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| diff -r 608ea80cccba -r 41faa653d86c dedup.xml --- a/dedup.xml Fri Jul 25 13:54:54 2025 +0000 +++ b/dedup.xml Wed Aug 13 20:05:12 2025 +0000 |
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| b'@@ -1,15 +1,27 @@\n-<tool id="pairtools_dedup" name="Pairtools dedup" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">\n+<tool id="pairtools_dedup" name="Pairtools dedup" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE_VERSION@" license="MIT">\n <description>Find and remove PCR/optical duplicates</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n <expand macro="requirements"/>\n <command detect_errors="exit_code"><![CDATA[\n+ #if $pairs_path.is_of_type(\'4dn_pairs.gz\') or $pairs_path.is_of_type(\'4dn_pairsam.gz\'):\n+ #set $input_link = "input.gz"\n+ #set $output_dedup_pairs_link = "output_dedup_pairs.ga"\n+ #set $output_dups_pairs_link = "output_dups_pairs.gz"\n+ #else\n+ #set $input_link = "input"\n+ #set $output_dedup_pairs_link = "output_dedup_pairs"\n+ #set $output_dups_pairs_link = "output_dups_pairs"\n+ #end if\n+ ln -s \'$pairs_path\' \'$input_link\' &&\n+ ln -s \'$output_dedup_pairs\' \'$output_dedup_pairs_link\' &&\n+ ln -s \'$output_dups_pairs\' \'$output_dups_pairs_link\' &&\n pairtools dedup\n- \'$pairs_path\'\n- -o \'$output_dedup_pairs\'\n+ \'$input_link\'\n+ -o \'$output_dedup_pairs_link\'\n #if $output_dups:\n- --output-dups \'$output_dups_pairs\'\n+ --output-dups \'$output_dups_pairs_link\'\n #end if\n $mark_dups\n #if $output_stats:\n@@ -24,16 +36,17 @@\n --max-mismatch ${max_mismatch}\n ]]></command>\n <inputs> \n- <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam" label="Input pairs file" help="Input triu-flipped sorted .pairs or .pairsam file"/>\n+ <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam,4dn_pairs.gz,4dn_pairsam.gz" label="Input pairs file" help="Input triu-flipped sorted .pairs or .pairsam file"/>\n <param argument="--mark-dups" type="boolean" truevalue="--mark-dups" falsevalue="" checked="True" label="Duplicate pairs are marked as DD in pair_type and as a duplicate in the SAM entries"/>\n <param argument="--output-dups" type="boolean" truevalue="--output-dups" falsevalue="" checked="False" label="Output file for duplicate pairs"/>\n <param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Output file for duplicate statistics"/>\n <param argument="--max-mismatch" type="integer" value="3" min="0" label="Maximum number of mismatches. Pairs with both sides mapped within this distance "bp" from each other are considered duplicates."/>\n <param argument="--output-bytile-stats" type="boolean" truevalue="--output-bytile-stats" falsevalue="" checked="False" label="Output file for optical duplicate statistics for datasets with original Illumina-generated read IDs."/>\n+ <param name="compress_output" type="boolean" truevalue=".gz" falsevalue="" checked="false" label="Compress output files" />\n </inputs>\n <outputs>\n- <data name="output_dedup_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Deduplicated Pairs"/>\n- <data name="output_dups_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Duplicate Pairs">\n+ <data name="output_dedup_pairs" label="${tool.name} on ${on_string}: Deduplicated Pairs" format_source="pairs_path" />\n+ <data name="output_dups_pairs" label="${tool.name} on ${on_string}: Duplicate Pairs" format_source="pairs_path" >\n <filter>output_dups</filter>\n </data>\n <data name="dedup_pairs_stats" format="tabular" label="${tool.name} on ${on_string}: Deduplicated stats">\n@@ -44,46 +57,67 @@\n </data>\n </outputs>\n <tests>\n- \n <!--Test 01 with default parameters-->\n <test expect_num_outputs="1">\n- <param name="pair'..b'<param name="mark_dups" value="true"></param>\n <param name="output_stats" value="true"></param>\n- <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" lines_diff="20"/>\n- <output name="dedup_pairs_stats" file="output_dedup_pairs.stats" lines_diff="20"/>\n+ <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" ftype="4dn_pairsam" lines_diff="20"/>\n+ <output name="dedup_pairs_stats" file="output_dedup_pairs.stats" ftype="tabular" lines_diff="20"/>\n </test>\n- <!--Test 04 mark_dups and output_stats enabled, max_mismatch set to 0-->\n+ <!--Test 06 mark_dups and output_stats enabled, max_mismatch set to 0-->\n <test expect_num_outputs="2">\n- <param name="pairs_path" value="output_sorted_pairs.pairsam"/>\n+ <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>\n <param name="mark_dups" value="true"></param>\n <param name="output_stats" value="true"></param>\n <param name="max_mismatch" value="0"></param>\n- <output name="output_dedup_pairs" file="output_dedup_max_mismatch0_sorted.pairsam" lines_diff="20"/>\n- <output name="dedup_pairs_stats" file="output_dedup_max_mismatch0_sorted.stats" lines_diff="20"/>\n+ <output name="output_dedup_pairs" file="output_dedup_max_mismatch0_sorted.pairsam" ftype="4dn_pairsam" lines_diff="20"/>\n+ <output name="dedup_pairs_stats" file="output_dedup_max_mismatch0_sorted.stats" ftype="tabular" lines_diff="20"/>\n </test>\n- <!--Test 05 mark_dups and output_stats + bytile_stats enabled-->\n+ <!--Test 07 mark_dups and output_stats + bytile_stats enabled-->\n <test expect_num_outputs="3">\n- <param name="pairs_path" value="output_sorted_pairs.pairsam"/>\n+ <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>\n <param name="mark_dups" value="true"></param>\n <param name="output_stats" value="true"></param>\n <param name="output_bytile_stats" value="true"></param>\n- <output name="output_dedup_pairs" file="output_dedup_max_parent_id_bytile_sorted.pairsam" lines_diff="20"/>\n- <output name="dedup_pairs_stats" file="output_dedup_max_parent_id_bytile_sorted.stats" lines_diff="20"/>\n- <output name="dedup_bytile_stats" file="output_dedup_max_parent_id_bytile_sorted_tile_dups.stats" lines_diff="20"/>\n+ <output name="output_dedup_pairs" file="output_dedup_max_parent_id_bytile_sorted.pairsam" ftype="4dn_pairsam" lines_diff="20"/>\n+ <output name="dedup_pairs_stats" file="output_dedup_max_parent_id_bytile_sorted.stats" ftype="tabular" lines_diff="20"/>\n+ <output name="dedup_bytile_stats" file="output_dedup_max_parent_id_bytile_sorted_tile_dups.stats" ftype="tabular" lines_diff="20"/>\n+ </test>\n+ <!--Test 08 mark_dups and output_stats + bytile_stats enabled, compress output-->\n+ <test expect_num_outputs="3">\n+ <param name="pairs_path" ftype="4dn_pairsam" value="output_sorted_pairs.pairsam"/>\n+ <param name="mark_dups" value="true"></param>\n+ <param name="output_stats" value="true"></param>\n+ <param name="compress_output" value="true"></param>\n+ <param name="output_bytile_stats" value="true"></param>\n+ <output name="output_dedup_pairs" file="output_dedup_max_parent_id_bytile_sorted.pairsam" ftype="4dn_pairsam" decompress="true" lines_diff="20"/>\n+ <output name="dedup_pairs_stats" file="output_dedup_max_parent_id_bytile_sorted.stats" ftype="tabular" decompress="true" lines_diff="20"/>\n+ <output name="dedup_bytile_stats" file="output_dedup_max_parent_id_bytile_sorted_tile_dups.stats" ftype="tabular" decompress="true" lines_diff="20"/>\n </test>\n </tests>\n <help><![CDATA[\n' |
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| diff -r 608ea80cccba -r 41faa653d86c macros.xml --- a/macros.xml Fri Jul 25 13:54:54 2025 +0000 +++ b/macros.xml Wed Aug 13 20:05:12 2025 +0000 |
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| @@ -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> |
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| diff -r 608ea80cccba -r 41faa653d86c test-data/output_dedup_pairs_markdups.pairsam.gz |
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| diff -r 608ea80cccba -r 41faa653d86c test-data/output_parsed_pairs_sam.pairs.gz |
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| diff -r 608ea80cccba -r 41faa653d86c test-data/output_parsed_pairs_sam_assemblyname.pairs.gz |
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| diff -r 608ea80cccba -r 41faa653d86c test-data/output_sorted_pairs.pairsam.gz |
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