Mercurial > repos > proteore > proteore_venn_diagram
changeset 4:c3bbc688dde2 draft
planemo upload commit 1316c2feac23e3b1a4f929c3386142d5d5d7e37a-dirty
| author | proteore |
|---|---|
| date | Mon, 13 May 2019 09:55:45 -0400 |
| parents | 1645a66fd0ee |
| children | 5f8462a9de89 |
| files | venn_diagram.py venn_diagram.xml |
| diffstat | 2 files changed, 101 insertions(+), 61 deletions(-) [+] |
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--- a/venn_diagram.py Thu Dec 13 04:19:23 2018 -0500 +++ b/venn_diagram.py Mon May 13 09:55:45 2019 -0400 @@ -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
--- a/venn_diagram.xml Thu Dec 13 04:19:23 2018 -0500 +++ b/venn_diagram.xml Mon May 13 09:55:45 2019 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="Jvenn" name="Venn diagram" version="2018.12.12"> +<tool id="Jvenn" name="Venn diagram" version="2019.05.13"> <description>[JVenn] </description> <command><![CDATA[ @@ -8,41 +8,53 @@ #for $i, $s in enumerate($series) --input #if $s.se.input == "file" - "$s.se.file" "$s.se.name" "file" "$s.se.header" "$s.se.ncol" + "$s.se.file" "$s.name" "file" "$s.se.header" "$s.se.ncol" #else - "$s.se.list" "$s.se.name" "list" + "$s.se.list" "$s.name" "list" #end if #end for --summary "$output_summary" ]]></command> <inputs> <!-- Files --> - <repeat name="series" title="Lists to compare" min="2" max="6" > + <repeat name="series" title="List to compare" min="2" max="6" > <conditional name="se" > - <param type="select" name="input" label="Please provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" > - <option value="list">Copy/paste your identifiers </option> - <option value="file" selected="true">Input file containing your identifiers</option> - </param> - <when value="file"> - <param type="data" name="file" format="txt,tabular" label="Choose a file that contains your list of IDs" /> - <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> - <param type="text" name="ncol" value="c1" label="Please specify the column where you would like to apply the comparison" help ='For example, fill in "c1" if you want to filter the first column' /> - <param type="text" name="name" value="" label="Please enter the name of this list" help="This name will be displayed on venn diagram" /> - </when> - <when value="list"> - <param type="text" name="list" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' > - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - </valid> - <mapping initial="none"> - <add source="'" target="__sq__"/> - </mapping> - </sanitizer> - </param> - <param type="text" name="name" value="" label="Please enter the name of this list" help="This name will be displayed on venn diagram" /> - </when> - </conditional> + <param type="select" name="input" label="Enter your list" help="Copy/paste or from a file (e.g. table)" > + <option value="list">Copy/paste list </option> + <option value="file" selected="true">Input file containing your list</option> + </param> + <when value="file"> + <param type="data" name="file" format="txt,tabular" label="Select your file" /> + <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> + <param type="text" name="ncol" value="c1" label="Column number on which apply the comparison" help ='For example, fill in "c1" if you want to filter the first column'> + <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> + </param> + </when> + <when value="list"> + <param type="text" name="list" label="Copy/paste list" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' > + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="/"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </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" optional="false"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + <validator type="regex" message="Please enter a list name">[a-zA-Z0-9._-]+</validator> + </param> </repeat> </inputs> <outputs> @@ -82,42 +94,67 @@ <output name="output_text" file="Venn_text_output.txt" /> </test> </tests> - <help> + <help><![CDATA[ + +**Description** -This tool draw a venn diagram from lists/files using Jvenn plug-in (http://jvenn.toulouse.inra.fr/app/index.html). It also creates output files that contain common or specific elements between query and each compared lists/files. +This tool is used for cross-comparison purpose between several lists having a common key (e.g. IDs) and draw a venn diagram from lists/files using the Jvenn plug-in (see Authors below). +It also creates output text file that contain common or specific elements between query and each compared lists/files. + +----- **Inputs** -* **Query file:** A file containing different information of proteins, could be output of previous components. +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 -* **File of a list of IDs:** .TXT format, each line contains 1 ID +* **List of IDs in a copy/paste mode:** IDs have to be separated by a space (e.g. AMY1A ALB IGKC CSTA IGHA1 ACTG1) + +* **for example an IDs list file** in .txt format, with 1 ID per line - AMY1A +.. csv-table:: tab1 + :header: "Ids" + - ALB - - IGKC + "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. - CSTA +Ids in a line will be split by ";", so if you have this kind of input : - IGHA1 +.. csv-table:: tab with multiple ids per line + :header: "Ids" - ACTG1 - -* **List of IDs:** IDs separated by a space + "P22531" + "P04792" + "P01834" + "Q96KK5" + "Q06830;P60709;P13646;P31949" + "P06702" + "P14923" + "Q13835" - AMY1A ALB IGKC CSTA IGHA1 ACTG1 +All ids will be used (Q06830,P60709,P13646 and P31949 will be split). -If you choose a file, it is necessary to specify the column where you would like to perform the comparison. +----- -**Outputs** +**Parameter** + +"Please enter the name of this list": each list or set should be named, this information will be reported in both output (see below) + +----- -* **Summary file** (venn_diagram_summary.html): - Venn diagram: Could be downloaded as image (PNG, SVG) +**Output** -* **Venn text output file** - A text file containing common/specific elements among compared lists/files. - +Two outputs are generated: + +* **Graphical file**: Venn diagram that you can either display (interactive mode) or download as image (PNG, SVG format) + +* **Venn text output file** : a text file containing specific elements or shared by lists/files. + ----- .. class:: infomark @@ -135,8 +172,7 @@ 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> - <citations> - </citations> +]]></help> + <citations> + </citations> </tool>