# HG changeset patch
# User lain
# Date 1643737087 0
# Node ID 10266818794ba285a2b5b264b5f0d836e2a71f15
# Parent  85b4593da2713ce3b4fe451bfdff2ba9043d3f96
Uploaded

diff -r 85b4593da271 -r 10266818794b XSeeker.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/XSeeker.xml	Tue Feb 01 17:38:07 2022 +0000
@@ -0,0 +1,71 @@
+<tool id="interactive_tool_xseeker" tool_type="interactive" name="xseeker" version="1.4.0">
+    <description>Visualization and annotation of LC-MSMS data tool</description>
+    <requirements>
+        <container type="docker">emetabohub/xseeker:1.4.0</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="XSeeker visualisation of $infile.display_name" requires_domain="True">
+            <port>8765</port>
+            <url>/</url>
+        </entry_point>
+    </entry_points>
+    <environment_variables>
+        <environment_variable name="HISTORY_ID" strip="True">$__history_id__</environment_variable>
+        <environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable>
+        <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
+        <environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable>
+        <environment_variable name="API_KEY" strip="True">
+            #if $__user__:
+                #for $api_key in $__user__.api_keys:
+                    ${api_key.key}
+                    #break
+                #end for
+            #end if
+        </environment_variable>
+        <environment_variable name="DOCKER">TRUE</environment_variable>
+    </environment_variables>
+    <command><![CDATA[
+        ln -s ${infile} /XSeeker/input/test.sqlite
+        &&  /entrypoint.sh
+    ]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="binary" label="An sqlite file processed by XSeeker Preprocessor"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+XSeeker is a tool to visualise and annote data from LC-MSMS.
+
+The prefered workflows to process your data is:
+
+{mzxml} -> xcms{rdata} -> camera{rdata} -> XSeekerPreparator{sqlite} -> XSeeker
+
+But it is still possible to only do:
+
+{mzxml} -> xcms{rdata} -> camera{rdata} -> XSeeker
+
+This way, you will have to choose the files you want to visualize, but it will take some time to import them.
+
+XSeeker can output csv, tsv and mzTab files, so annotations can be used in other programs and/or is human readable/writable.
+
+XSeeker can also output an sqlite file, exactly like the one it takes in input. This file can be used to stop your anotation and resume the process later. It's like an XSeeker save file.
+
+
+]]>
+    </help>
+    <citations>
+       <citation type="bibtex">
+       @misc{
+            author       = {Lain Pavot - lain.pavot@inrae.fr },
+            title        = {{XSeeker -  A tool to visualise and annote data from LC-MSMS }},
+            publisher    = {INRAE},
+            url          = {}
+        }
+    }</citation>
+    </citations>
+</tool>