| Previous changeset 3:62aebaf6cfa0 (2019-05-10) Next changeset 5:99a5ed06b86c (2019-06-24) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 4b572d4605dfc1d5cfe2b46c9f0061d041e63df9 |
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modified:
catWrapper.xml |
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| diff -r 62aebaf6cfa0 -r 7afc0515a307 catWrapper.xml --- a/catWrapper.xml Fri May 10 10:15:02 2019 -0400 +++ b/catWrapper.xml Tue Jun 18 11:59:06 2019 -0400 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.2.0">\n+<tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.3.0">\n <description>tail-to-head by specifying how</description>\n <command><![CDATA[\n #if $headers == 0:\n@@ -8,11 +8,14 @@\n #end if\n #if $global_condition.input_type == "singles":\n #if $dataset_names == "No":\n- $concat_command\n #for $file in $global_condition.inputs\n- \'$file\'\n+ #if $file.ext[-2:] == "gz":\n+ gzip -dc \'$file\' | $concat_command | gzip -c >> \'$out_file1\' &&\n+ #else:\n+ $concat_command \'$file\' >> \'$out_file1\' &&\n+ #end if\n #end for\n- > \'$out_file1\'\n+ sleep 1\n #else:\n #for $file in $global_condition.inputs\n #if $file.ext[-2:] == "gz":\n@@ -26,15 +29,19 @@\n sleep 1\n #end if\n #else if $global_condition.input_type == "simple_collections":\n- #if $global_condition.collections_condition.collection_cat_type == "two_collections":\n mkdir concatenated &&\n #if $dataset_names == "No":\n- #for $x, $y in zip($global_condition.collections_condition.input_1, $global_condition.collections_condition.input_2)\n- $concat_command \'$x\' \'$y\' > concatenated/\'${x.element_identifier}.listed.${x.ext}.listed\' &&\n+ #for $x, $y in zip($global_condition.input_1, $global_condition.input_2):\n+ #if $x.ext[-2:] == "gz":\n+ gzip -dc \'$x\' | $concat_command | gzip -c > concatenated/\'${x.element_identifier}.listed.${x.ext}.listed\' &&\n+ gzip -dc \'$y\' | $concat_command | gzip -c >> concatenated/\'${x.element_identifier}.listed.${x.ext}.listed\' &&\n+ #else:\n+ $concat_command \'$x\' \'$y\' > concatenated/\'${x.element_identifier}.listed.${x.ext}.listed\' &&\n+ #end if\n #end for\n sleep 1\n #else:\n- #for $x, $y in zip($global_condition.collections_condition.input_1, $global_condition.collections_condition.input_2)\n+ #for $x, $y in zip($global_condition.input_1, $global_condition.input_2)\n #if $x.ext[-2:] == "gz":\n printf "# ${x.element_identifier}\\n" | gzip -c > concatenated/\'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed\' &&\n gzip -dc \'$x\' | $concat_command | gzip -c >> concatenated/\'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed\' &&\n@@ -49,82 +56,142 @@\n #end for\n sleep 1\n #end if\n- #end if\n #else if $global_condition.input_type == "paired_collection":\n #if $global_condition.paired_cat_type == "by_strand":\n+ mkdir concatenated &&\n #if $dataset_names == "No":\n #for $file in $global_condition.inputs\n- $concat_command\n- $file[\'forward\']\n- >> \'$forward\' &&\n- $concat_command\n- $file[\'reverse\']\n- >> \'$reverse\' &&\n+ #if $file[\'forward\'].ext[-2:] == "gz":\n+ gzip -dc $file[\'forward\'] | $concat_command | gzip -c >> concatenated/forward.listed.${file[\'forward\'].ext}.listed &&\n+ gzip -dc $file[\'reverse\'] | $concat_command | gzip -c >> concatenated/reverse.listed.${file[\'reverse\'].ext}.listed &&\n+ #else:\n+ $concat_command $file[\''..b'ections\') or (global_condition[\'input_type\'] == \'nested_collection\')</filter>\n </collection>\n </outputs>\n <tests>\n@@ -322,6 +388,48 @@\n <element name="1_f.fastq_1_r.fastq" file="1_options.fastq.gz" decompress="True"/>\n </output_collection>\n </test>\n+ <test> <!-- Test nested collections concatenation -->\n+ <param name="input_type" value="nested_collection" />\n+ <param name="inputs">\n+ <collection type="list:list">\n+ <element name="2">\n+ <collection type="list">\n+ <element name="2_f" value="2_f.fastq" ftype="fastq"/>\n+ <element name="2_r" value="2_r.fastq" ftype="fastq"/>\n+ </collection>\n+ </element>\n+ <element name="3">\n+ <collection type="list">\n+ <element name="3" value="3.fastq" ftype="fastq"/>\n+ </collection>\n+ </element>\n+ </collection>\n+ </param>\n+ <param name="dataset_names" value="No" />\n+ <param name="headers" value="0" />\n+ <output_collection name="list_output" type="list" count="2" >\n+ <element name="2" file="2.fastq"/>\n+ <element name="3" file="3.fastq"/>\n+ </output_collection>\n+ </test>\n+ <test> <!-- Test 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+ <element name="1">\n+ <collection type="list">\n+ <element name="1_f.fastq" value="1_f.fastq.gz" ftype="fastq.gz"/>\n+ <element name="1_r.fastq" value="1_r.fastq.gz" ftype="fastq.gz"/>\n+ </collection>\n+ </element>\n+ </collection>\n+ </param>\n+ <param name="dataset_names" value="Yes" />\n+ <param name="headers" value="4" />\n+ <output_collection name="list_output" type="list" count="1" >\n+ <element name="1" file="1_options.fastq.gz" decompress="True"/>\n+ </output_collection>\n+ </test>\n </tests>\n <help>\n \n@@ -329,9 +437,9 @@\n \n **WARNING:** This tool does not check if the datasets being concatenated are in the same format.\n \n-**WARNING:** The paired collection operations do not handle gziped files.\n+**WARNING:** When concatenating 2 collections make sure the first collection is the one with the most items.\n \n-**WARNING:** When concatenating 2 collections make sure the first collection is the one with the most items.\n+**WARNING:** This tool can\'t handle nested collection deeper than list:list.\n \n -----\n \n@@ -349,6 +457,8 @@\n \n - When the inputs are 2 collections: datasets are concatenated in a pairwise combination and a single dataset collection is returned\n \n+ - When nested collection concatenation: datasets in each sub-collection are concatenated and a simple dataset collection is returned\n+\n - Skipping lines before concatenation to avoid headers\n \n - Add the name of the concatenated files as separator\n@@ -456,6 +566,32 @@\n \n -----\n \n+**Nested collection concatenation example**\n+\n+Nested collection:\n+\n+ - Experiment\n+\n+ - Sample_1\n+\n+ - Sample_1_file_1\n+ - Sample_1_file_2\n+\n+ - Sample_2\n+\n+ - Sample_2_file_1\n+ - Sample_2_file_2\n+ - Sample_2_file_3\n+\n+Concatenation result::\n+\n+ A single collection containing:\n+\n+ - Sample_1: (Sample_1_file_1 + Sample_1_file_2)\n+ - Sample_2: (Sample_2_file_1 + Sample_2_file_2 + Sample_2_file_3)\n+\n+-----\n+\n **When selecting "Include dataset names" when concatenating files**:\n \n 1rst file name="first_tabular"::\n' |