| Previous changeset 2:1fe4d165ac0e (2019-04-15) Next changeset 4:7afc0515a307 (2019-06-18) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 64e9762ab35b04bb0d151e441baa2fae8bf2cb4a |
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modified:
catWrapper.xml |
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| diff -r 1fe4d165ac0e -r 62aebaf6cfa0 catWrapper.xml --- a/catWrapper.xml Mon Apr 15 18:52:43 2019 -0400 +++ b/catWrapper.xml Fri May 10 10:15:02 2019 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.1.0">\n+<tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.2.0">\n <description>tail-to-head by specifying how</description>\n <command><![CDATA[\n #if $headers == 0:\n@@ -25,6 +25,31 @@\n #end for\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+ #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+ #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+ printf "# ${y.element_identifier}\\n" | gzip -c >> concatenated/\'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed\' &&\n+ gzip -dc \'$y\' | $concat_command | gzip -c >> concatenated/\'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed\' &&\n+ #else:\n+ printf "# ${x.element_identifier}\\n" > concatenated/\'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed\' &&\n+ $concat_command \'$x\'>> concatenated/\'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed\' &&\n+ printf "# ${y.element_identifier}\\n" >> concatenated/\'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed\' &&\n+ $concat_command \'$y\' >> concatenated/\'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed\' &&\n+ #end if\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 #if $dataset_names == "No":\n@@ -107,19 +132,31 @@\n <conditional name="global_condition">\n <param name="input_type" type="select" label="What type of data do you wish to concatenate?" help="Depending on the type of input selected the concatenation options will differ">\n <option value="singles">Single datasets</option>\n+ <option value="simple_collections">Collections</option>\n <option value="paired_collection">Paired 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 </when>\n <when value="paired_collection">\n- <param name="inputs" type="data_collection" collection_type="list:paired" label="Input paired collections to concatenate"/>\n+ <param name="inputs" type="data_collection" collection_type="list:paired" 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">Conca'..b'ections 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+ <element name="3" value="3_f.fastq"/>\n+ <element name="4" value="4_f.fastq"/>\n+ </collection>\n+ </param>\n+ <param name="input_2">\n+ <collection type="list">\n+ <element name="2" value="2_r.fastq"/>\n+ <element name="3" value="3_r.fastq"/>\n+ <element name="4" value="4_r.fastq"/>\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="3" >\n+ <element name="2" file="2.fastq"/>\n+ <element name="3" file="3.fastq"/>\n+ <element name="4" file="4.fastq"/>\n+ </output_collection>\n+ </test>\n+ <test> <!-- Test 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" value="1_f.fastq.gz"/>\n+ </collection>\n+ </param>\n+ <param name="input_2">\n+ <collection type="list">\n+ <element name="1_r.fastq" value="1_r.fastq.gz"/>\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_f.fastq_1_r.fastq" file="1_options.fastq.gz" decompress="True"/>\n+ </output_collection>\n+ </test>\n </tests>\n <help>\n \n@@ -250,13 +331,23 @@\n \n **WARNING:** The paired collection operations do not handle gziped files.\n \n+**WARNING:** When concatenating 2 collections make sure the first collection is the one with the most items.\n+\n -----\n \n **What it does**\n \n Concatenates datasets and paired collections with multiple options:\n \n- - It\'s possible select either a concatenation by strand, by pair or a whole collection concatenation, when the input is a paired collection.\n+ - When the input is a paired collection:\n+\n+ - concatenation by strand : forward and reverse datasets are concatenated separately and a list with a single forward - reverse dataset pair is returned\n+\n+ - concatenation by pair : forward - reverse dataset pairs are concatenated and a simple dataset collection is returned\n+\n+ - whole collection concatenation : all datasets in the collection are concatenated and a single dataset is returned\n+\n+ - When the inputs are 2 collections: datasets are concatenated in a pairwise combination and a single dataset collection is returned\n \n - Skipping lines before concatenation to avoid headers\n \n@@ -294,6 +385,33 @@\n \n -----\n \n+**2 Collections concatenation**\n+\n+1rst collection::\n+\n+ a\n+ b\n+ c\n+ d\n+\n+2nd collection::\n+\n+ 1\n+ 2\n+ 3\n+ 4\n+\n+Concatenation result::\n+\n+ A single collection containing:\n+\n+ a concatenated with 1\n+ b concatenated with 2\n+ c concatenated with 3\n+ d concatenated with 4\n+\n+-----\n+\n **Paired collection concatenation example**\n \n 1rst pair::\n@@ -304,7 +422,7 @@\n \n forward - reverse\n \n-Concatenation by strand::\n+- Concatenation by strand::\n \n concatenates:\n \n@@ -315,7 +433,7 @@\n \n 1 pair\n \n-Concatenation by pair::\n+- Concatenation by pair::\n \n concatenates:\n \n@@ -326,7 +444,7 @@\n \n 2 datasets\n \n-Concatenate all::\n+- Concatenate all::\n \n concatenates:\n \n' |