# HG changeset patch # User metaboflow_cam # Date 1569315397 14400 # Node ID 6195ef2417aad48585e9a6257eafd24e17de28b8 Uploaded diff -r 000000000000 -r 6195ef2417aa isolab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/isolab Tue Sep 24 04:56:37 2019 -0400 @@ -0,0 +1,1131 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GitHub - wanchanglin/isolab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + pkgs + + + pass all planemo test + + + Mar 27, 2019 +
+ + + + test-data + + + more planemo test + + + Apr 2, 2019 +
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+ + + + README.md + + + README + + + Mar 28, 2019 +
+ + + + isolab.R + + + pass all planemo test + + + Mar 27, 2019 +
+ + + + isolab.xml + + + more planemo test + + + Apr 2, 2019 +
+ + + + macros.xml + + + more planemo test + + + Apr 2, 2019 +
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+ + README.md +

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+

isolab for Galaxy

+

This is Galaxy tool for R package +IsotopicLabelling +which analyses mass spectrometric isotopic patterns obtained following +isotopic labelling experiments. For more details, see the +IsotopicLabelling: an R package for the analysis of MS isotopic patterns of +labelled +analytes.

+

Installation

+
    +
  • +

    Install Galaxy under Linux.

    +
    • +
  • +

    Install conda under +Linux. conda is used to install requirements of this tool.

    +
    • +
  • +

    Use git to clone this tool

    +
    git clone https://github.com/wanchanglin/isolab.git
    +
    • +
  • +

    Add this tool's location into Galaxy' tool config file: +~/Galaxy/config/tool_conf.xml. For example, one simplified +tool_conf.xml looks like:

    +
    <?xml version='1.0' encoding='utf-8'?>
+<toolbox monitor="true">
+  
+  <section id="getext" name="Get Data">
+    <tool file="data_source/upload.xml" />
+  </section>
+  
+  <section id="MyTools" name="My Tools">
+    <tool file="/path/to/isolab/isolab.xml" />
+  </section>
+
+</toolbox>
    +
    • +
  • +

    The Galaxy tool uses R packages optparse, +WriteXLS and gsubfn. All of these packages will be installed by +conda in its virtual environment. Two R packages IsotopicLabelling and +ecipes are already included.

    +
    • +
  • +

    Some test data are located in test-data.

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    • +
+

Notes

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  • planemo test compares the history results in test-data/res produced by +shell scripts in test. (27-03-2019, Wed)
    • +
  • White spaces in groups input: Group factor delimiter is comma. No any +extra white spaces are allowed otherwise an error will be encountered. +Note that isolab.sh has no problem with white spaces. Probably it is +'Cheetah' or Galaxy's text input problem. (31-05-2018, Thu)
    • +
+

Authors, contributors & contacts

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