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Commit message:
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/extract_element_from_collection commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 |
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added:
extract_element_from_collection.xml test-data/example.mothur.shared test-data/multisample.taxonomy |
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| diff -r 000000000000 -r c46360dcbf3f extract_element_from_collection.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract_element_from_collection.xml Wed Dec 13 10:09:11 2017 -0500 |
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| @@ -0,0 +1,62 @@ +<tool id="extract_element_from_collection" name="Extract Element" version="0.1" profile="16.07"> + <description>from a collection based on name</description> + <command detect_errors="aggressive"><![CDATA[ + echo 'no element with name $elementname found in your collection' > '$output' + + && mkdir elementoutputs + #for $dataset in $input_collection: + && echo $dataset.element_identifier + #if $elementname == '' + && cp $dataset 'elementoutputs/$dataset.element_identifier' + #elif $dataset.element_identifier == $elementname: + && cp $dataset '$output' + #end if + #end for + ]]></command> + <inputs> + <param name="input_collection" type="data_collection" collection_type="list" label="Input Collection"/> + <!-- find a way to make a select from all elements? --> + <param name="elementname" type="text" value="" label="name of collection element to extract" help="if left blank, all files will be extracted"/> + </inputs> + <outputs> + <data name="output" format="auto" label="${elementname}"> + <filter>elementname != ''</filter> + </data> + <data format="auto" name="extracted"> + <discover_datasets pattern="(?P<designation>.+)" directory="elementoutputs" visible="true" assign_primary_output="true"/> + <filter>elementname == ''</filter> + </data> + </outputs> + <tests> + <test><!-- test with valid element --> + <param name="input_collection"> + <collection type="list"> + <element name="element1" value="example.mothur.shared" /> + <element name="element2" value="multisample.taxonomy" /> + </collection> + </param> + <param name="elementname" value="element2"/> + <output name="output" file="multisample.taxonomy"/> + </test> + <test><!-- test with invalid element --> + <param name="input_collection"> + <collection type="list"> + <element name="element1" value="example.mothur.shared" /> + <element name="element2" value="multisample.taxonomy" /> + </collection> + </param> + <param name="elementname" value="element3"/> + <output name="output"> + <assert_contents> + <has_text text="no element with name"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**What it does** +extract a dataset from a collection based on name + ]]></help> + <citations> + </citations> +</tool> |
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| diff -r 000000000000 -r c46360dcbf3f test-data/example.mothur.shared --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.mothur.shared Wed Dec 13 10:09:11 2017 -0500 |
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|
| b |
| diff -r 000000000000 -r c46360dcbf3f test-data/multisample.taxonomy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multisample.taxonomy Wed Dec 13 10:09:11 2017 -0500 |
| b |
| b'@@ -0,0 +1,335 @@\n+OTU\tSize\tTaxonomy\n+Otu0001\t6675\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0002\t5145\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0003\t4815\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0004\t4283\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0005\t4060\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0006\t3710\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0007\t2489\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);Bacteroidaceae(100);Bacteroides(100);\n+Otu0008\t2152\tBacteria(100);Firmicutes(100);Bacilli(100);Lactobacillales(100);Lactobacillaceae(100);Lactobacillus(100);\n+Otu0009\t1581\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0010\t1572\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);Rikenellaceae(100);Alistipes(100);\n+Otu0011\t1539\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0012\t1416\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0013\t1092\tBacteria(100);Firmicutes(100);Erysipelotrichia(100);Erysipelotrichales(100);Erysipelotrichaceae(100);Turicibacter(100);\n+Otu0014\t980\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0015\t632\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Blautia(100);\n+Otu0016\t553\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0017\t470\tBacteria(100);Firmicutes(100);Bacilli(100);Lactobacillales(100);Lactobacillaceae(100);Lactobacillus(100);\n+Otu0018\t462\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0019\t414\tBacteria(100);Firmicutes(100);Bacilli(100);Lactobacillales(100);Lactobacillaceae(100);Lactobacillus(94);\n+Otu0020\t395\tBacteria(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);\n+Otu0021\t330\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0022\t316\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Blautia(100);\n+Otu0023\t308\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Blautia(96);\n+Otu0024\t304\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Blautia(100);\n+Otu0025\t259\tBacteria(100);Tenericutes(100);Mollicutes(100);RF9(100);unclassified(100);unclassified(100);\n+Otu0026\t259\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0027\t257\tBacteria(100);Firmicutes(96);Clostridia(96);Clostridiales(96);Lachnospiraceae(96);unclassified(96);\n+Otu0028\t229\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Blautia(99);\n+Otu0029\t222\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0030\t220\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);unclassified(62);\n+Otu0031\t205\tBacteria(100);Actinobacteria(100);Actinobacteria(100);Bifidobacteriales(100);Bifidobacteriaceae(100);Bifidobacterium(100);\n+Otu0032\t203\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Clostridiaceae_1(100);Clostridium_sensu_stricto_1(100);\n+Otu0033\t203\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0034\t180\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(10'..b'ales(100);S24-7(100);unclassified(100);\n+Otu0300\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0301\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0302\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0303\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0304\t1\tBacteria(100);Firmicutes(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);\n+Otu0305\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0306\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0307\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0308\t1\tBacteria(100);Firmicutes(100);Bacilli(100);Lactobacillales(100);Lactobacillaceae(100);unclassified(100);\n+Otu0309\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0310\t1\tBacteria(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);\n+Otu0311\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0312\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Blautia(100);\n+Otu0313\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0314\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0315\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Eubacteriaceae(100);Anaerofustis(100);\n+Otu0316\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Anaerotruncus(100);\n+Otu0317\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0318\t1\tBacteria(100);Firmicutes(100);Bacilli(100);unclassified(100);unclassified(100);unclassified(100);\n+Otu0319\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);Bacteroidaceae(100);Bacteroides(100);\n+Otu0320\t1\tBacteria(100);Bacteroidetes(100);Flavobacteriia(100);Flavobacteriales(100);Cryomorphaceae(100);Fluviicola(100);\n+Otu0321\t1\tBacteria(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);\n+Otu0322\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0323\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Oscillibacter(100);\n+Otu0324\t1\tBacteria(100);Firmicutes(100);Bacilli(100);unclassified(100);unclassified(100);unclassified(100);\n+Otu0325\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0326\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0327\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0328\t1\tBacteria(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);\n+Otu0329\t1\tBacteria(100);Firmicutes(100);Bacilli(100);unclassified(100);unclassified(100);unclassified(100);\n+Otu0330\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0331\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0332\t1\tBacteria(100);Firmicutes(100);Bacilli(100);Bacillales(100);Listeriaceae(100);Listeria(100);\n+Otu0333\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0334\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Marvinbryantia(100);\n' |