| Previous changeset 7:55cf9d9defd1 (2019-07-09) Next changeset 9:5b1b635232ed (2024-06-13) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd |
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modified:
catWrapper.xml |
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| diff -r 55cf9d9defd1 -r 5b2cc63d7a21 catWrapper.xml --- a/catWrapper.xml Tue Jul 09 09:52:16 2019 -0400 +++ b/catWrapper.xml Fri Oct 13 09:46:58 2023 +0000 |
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| b'@@ -1,5 +1,5 @@\n-<tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.4.1">\n- <description>tail-to-head by specifying how</description>\n+<tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.4.2">\n+ <description>tail-to-head while specifying how</description>\n <command><![CDATA[\n #if $headers == 0:\n #set $concat_command = "cat"\n@@ -233,10 +233,12 @@\n <option value="nested_collection">Nested collection</option>\n </param>\n <when value="singles">\n- <param name="inputs" type="data" label="Concatenate Datasets" multiple="True" help="All inputed datasets will be concatenated tail-to-head."/>\n+ <param name="inputs" type="data" label="Concatenate Datasets" multiple="True" format="fastq,fastq.gz,txt,tabular,bed"\n+ help="All inputed datasets will be concatenated tail-to-head."/>\n </when>\n <when value="paired_collection">\n- <param name="inputs" type="data_collection" collection_type="list:paired" label="Input paired collection to concatenate"/>\n+ <param name="inputs" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz,txt,tabular,bed"\n+ label="Input paired collection to concatenate"/>\n <param name="paired_cat_type" type="select" label="What type of concatenation do you wish to perform?">\n <option value="by_strand">Concatenate all datsets of same strand (outputs a single pair of datasets)</option>\n <option value="by_pair">Concatenate pairs of datasets (outputs an unpaired collection of datasets)</option>\n@@ -262,45 +264,45 @@\n <filter>global_condition[\'input_type\'] == \'paired_collection\' and global_condition[\'paired_cat_type\'] == \'all\'</filter>\n </data>\n <collection name="paired_output" type="paired" label="Concatenation by strtand">\n- <discover_datasets pattern="(?P<name>.*)\\.listed\\.(?P<ext>.*)\\.listed" visible="false" directory="concatenated"/>\n+ <discover_datasets pattern="(?P<name>.*)\\.listed\\.(?P<ext>.*)\\.listed" format="fastq" visible="false" directory="concatenated"/>\n <filter>global_condition[\'input_type\'] == \'paired_collection\' and global_condition[\'paired_cat_type\'] == \'by_strand\'</filter>\n </collection>\n <collection name="list_output" type="list" label="Concatenation by pairs">\n- <discover_datasets pattern="(?P<identifier_0>.*)\\.listed\\.(?P<ext>.*)\\.listed" visible="false" directory="concatenated"/>\n+ <discover_datasets pattern="(?P<identifier_0>.*)\\.listed\\.(?P<ext>.*)\\.listed" format="fastq" visible="false" directory="concatenated"/>\n <filter>(global_condition[\'input_type\'] == \'paired_collection\' and global_condition[\'paired_cat_type\'] == \'by_pair\') or (global_condition[\'input_type\'] == \'simple_collections\') or (global_condition[\'input_type\'] == \'nested_collection\')</filter>\n </collection>\n </outputs>\n <tests>\n <!-- Single files concatenation -->\n- <test> <!-- Test 2 single files concatenation with no other option -->\n+ <test expect_num_outputs="1"> <!-- Test 1 single files concatenation with no other option -->\n <param name="input_type" value="singles" />\n <param name="inputs" value="1.bed,2.bed"/>\n <param name="dataset_names" value="No" />\n <param name="headers" value="0" />\n <output name="out_file1" file="cat_wrapper_out1.bed"/>\n </test>\n- <test> <!-- Test 2 single files concatenation with dataset names activated -->\n+ <test expect_num_outputs="1"> <!-- Test 2 single files concatenation with dataset names activated -->\n <param name="input_type" value="singles" />\n <param name="inputs" value="1.bed,2.be'..b'handling with no options -->\n <param name="input_type" value="singles" />\n <param name="inputs" value="1_f.fastq.gz,1_r.fastq.gz"/>\n <param name="dataset_names" value="No" />\n <param name="headers" value="0" />\n <output name="out_file1" file="1.fastq.gz" decompress="True"/>\n </test>\n- <test> <!-- Test gz handling with options -->\n+ <test expect_num_outputs="1"> <!-- Test 5 gz handling with options -->\n <param name="input_type" value="singles" />\n <param name="inputs" value="1_f.fastq.gz,1_r.fastq.gz"/>\n <param name="dataset_names" value="Yes" />\n@@ -308,7 +310,7 @@\n <output name="out_file1" file="1_options.fastq.gz" decompress="True"/>\n </test>\n <!-- Test paired options -->\n- <test> <!-- Test paired collection concatenation by_pair with no other option -->\n+ <test expect_num_outputs="1"> <!-- Test 6 paired collection concatenation by_pair with no other option -->\n <param name="input_type" value="paired_collection" />\n <param name="paired_cat_type" value="by_pair"/>\n <param name="inputs">\n@@ -341,7 +343,7 @@\n <element name="4" file="4.fastq"/>\n </output_collection>\n </test>\n- <test> <!-- Test paired collection concatenation by_strand with no other option -->\n+ <test expect_num_outputs="1"> <!-- Test 7 paired collection concatenation by_strand with no other option -->\n <param name="input_type" value="paired_collection" />\n <param name="paired_cat_type" value="by_strand"/>\n <param name="inputs">\n@@ -373,9 +375,8 @@\n <element name="reverse" file="r.fastq"/>\n </output_collection>\n </test>\n- <test> <!-- Test 2 collections concatenation -->\n+ <test expect_num_outputs="1"> <!-- Test 8 - 2 collections concatenation -->\n <param name="input_type" value="simple_collections" />\n- <param name="collection_cat_type" value="two_collections"/>\n <param name="input_1">\n <collection type="list">\n <element name="2" value="2_f.fastq"/>\n@@ -398,9 +399,8 @@\n <element name="4" file="4.fastq"/>\n </output_collection>\n </test>\n- <test> <!-- Test 2 collections concatenation with other options-->\n+ <test expect_num_outputs="1"> <!-- Test 9 - 2 collections concatenation with other options-->\n <param name="input_type" value="simple_collections" />\n- <param name="collection_cat_type" value="two_collections"/>\n <param name="input_1">\n <collection type="list">\n <element name="1_f.fastq.gz" value="1_f.fastq.gz"/>\n@@ -417,7 +417,7 @@\n <element name="1_f.fastq.gz_1_r.fastq.gz" file="1_options.fastq.gz" decompress="True"/>\n </output_collection>\n </test>\n- <test> <!-- Test nested collections concatenation -->\n+ <test expect_num_outputs="1"> <!-- Test 10 nested collections concatenation -->\n <param name="input_type" value="nested_collection" />\n <param name="inputs">\n <collection type="list:list">\n@@ -441,7 +441,7 @@\n <element name="3" file="3.fastq"/>\n </output_collection>\n </test>\n- <test> <!-- Test nested collections concatenation with options and gzip-->\n+ <test expect_num_outputs="1"> <!-- Test 11 nested collections concatenation with options and gzip-->\n <param name="input_type" value="nested_collection" />\n <param name="inputs">\n <collection type="list:list">\n@@ -672,4 +672,7 @@\n Adapted from galaxy\'s catWrapper.xml to allow multiple input files.\n \n </help>\n+ <citations>\n+ <citation type="doi">10.1186/gb-2010-11-8-r86</citation>\n+ </citations>\n </tool>\n' |