| Previous changeset 7:98b7912a9ceb (2019-03-05) Next changeset 9:72295909dccf (2019-09-12) |
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Commit message:
planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty |
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modified:
venn_diagram.py venn_diagram.xml |
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| diff -r 98b7912a9ceb -r bca31ac678f1 venn_diagram.py --- a/venn_diagram.py Tue Mar 05 11:25:31 2019 -0500 +++ b/venn_diagram.py Fri Jun 28 05:18:44 2019 -0400 |
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| @@ -47,20 +47,24 @@ if input_type == "file": header = inputs[i][3] ncol = inputs[i][4] - file_content = open(input_file, "r").readlines() + with open(input_file,"r") as handle : + file_content = csv.reader(handle,delimiter="\t") + file_content = list(file_content) #csv object to list - # Check if column number is in right form - if isnumber("int", ncol.replace("c", "")): - if header == "true": - file_content = [x.strip() for x in [line.split("\t")[int(ncol.replace("c", ""))-1].split(";")[0] for line in file_content[1:]]] # take only first IDs + # Check if column number is in right form + if isnumber("int", ncol.replace("c", "")): + if header == "true": + file_content = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content[1:]]] # gets ids from defined column + else: + file_content = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content]] else: - file_content = [x.strip() for x in [line.split("\t")[int(ncol.replace("c", ""))-1].split(";")[0] for line in file_content]] # take only first IDs - else: - raise ValueError("Please fill in the right format of column number") + raise ValueError("Please fill in the right format of column number") else: ids = set() file_content = inputs[i][0].split() + file_content = [x.split(";") for x in file_content] + file_content = [item.strip() for sublist in file_content for item in sublist if item != ''] #flat list of list of lists, remove empty items ids.update(file_content) if 'NA' in ids : ids.remove('NA') comp_dict[title] = ids |
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| diff -r 98b7912a9ceb -r bca31ac678f1 venn_diagram.xml --- a/venn_diagram.xml Tue Mar 05 11:25:31 2019 -0500 +++ b/venn_diagram.xml Fri Jun 28 05:18:44 2019 -0400 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="Jvenn" name="Venn diagram" version="2019.02.21"> +<tool id="Jvenn" name="Venn diagram" version="2019.06.27"> <description>[JVenn] </description> <command><![CDATA[ @@ -44,7 +44,7 @@ </param> </when> </conditional> - <param type="text" name="name" value="" label="Enter the name of this list" help="This name will be displayed on venn diagram"> + <param type="text" name="name" value="" label="Enter the name of this list" help="This name will be displayed on venn diagram" optional="false"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> @@ -53,6 +53,7 @@ <add source="'" target="__sq__"/> </mapping> </sanitizer> + <validator type="regex" message="Please enter a list name">[a-zA-Z0-9._-]+</validator> </param> </repeat> </inputs> @@ -102,7 +103,7 @@ ----- -**Inputs** +**Input** Can be either a list entered in a copy/paste mode or a single or multi-columns file (txt, tsv, csv, tab, output from other tools) up to six lists/files @@ -110,18 +111,38 @@ * **for example an IDs list file** in .txt format, with 1 ID per line -AMY1A - -ALB +.. csv-table:: tab1 + :header: "Ids" + -IGKC - -CSTA - -IGHA1 + "AMY1A" + "ALB" + "IGKC" + "CSTA" + "IGHA1" If you use a file as input list, it is necessary to specify the column number on which to apply the comparison. +Ids in a line will be split by ";", so if you have this kind of input : + +.. csv-table:: tab with multiple ids per line + :header: "Ids" + + "P22531" + "P04792" + "P01834" + "Q96KK5" + "Q06830;P60709;P13646;P31949" + "P06702" + "P14923" + "Q13835" + +All ID will be considered (i.e. Q06830,P60709,P13646 and P31949 will be split). + +.. class:: warningmark + +In copy/paste mode, the number of IDs considered in input is limited to 5000. + ----- **Parameter** @@ -134,7 +155,7 @@ Two outputs are generated: -* **Graphical file**: Venn diagram that you can either display (interactive mode) or download as image (PNG, SVG format) +* **Graphical file**: Venn diagram that you can either display (interactive mode) or download as an image (PNG, SVG format) * **Venn text output file** : a text file containing specific elements or shared by lists/files. @@ -150,11 +171,11 @@ **Galaxy integration** -T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR +Lien Nguyen, David Chistiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform -Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. +Help: contact@proteore.org for any questions or concerns about this tool. ]]></help> <citations> </citations> |