--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_export_samplemetadata.xml	Tue Oct 09 12:50:47 2018 -0400
@@ -0,0 +1,127 @@
+<tool id="xcms_export_samplemetadata" name="xcms get a sampleMetadata file" version="@WRAPPER_VERSION@.0">
+    <description>which need to be filled with extra information</description>
+
+    <macros>
+        <import>macros.xml</import>
+        <import>macros_xcms.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <command><![CDATA[
+        @COMMAND_RSCRIPT@/xcms_export_samplemetadata.r
+
+        images 'c("${"\",\"".join(map(str, $images))}")'
+    ]]></command>
+
+    <inputs>
+        <param name="images" type="data" format="rdata.xcms.findchrompeaks,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from multiple findChromPeaks" multiple="true" />
+    </inputs>
+
+    <outputs>
+        <data name="sampleMetadataOutput" format="tabular" label="sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" ftype="rdata"/>
+            <output name="sampleMetadataOutput" file="noclass.merged.sampleMetadata.tsv" />
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+@HELP_AUTHORS@
+
+=======================
+xcms get sampleMetadata
+=======================
+
+-----------
+Description
+-----------
+
+This tool generates a skeleton of sampleMetadata with perhaps some strange sample names which are definitely compatible with xcms and R
+
+This sampleMetadata file have to be filled with extra information as the class, batch information and maybe conditions
+
+-----------------
+Workflow position
+-----------------
+
+**Upstream tools**
+
+========================= ===================== ==============================
+Name                      Output file           Format
+========================= ===================== ==============================
+xcms.findChromPeaks       ``*``.raw.xset.RData  rdata.xcms.findchrompeaks
+------------------------- --------------------- ------------------------------
+xcms.findChromPeaks       ``*``.raw.xset.RData  rdata.xcms.findchrompeaks
+------------------------- --------------------- ------------------------------
+xcms.findChromPeaks       ``*``.raw.xset.RData  rdata.xcms.findchrompeaks
+------------------------- --------------------- ------------------------------
+...                       ...                   ...
+========================= ===================== ==============================
+
+
+**Downstream tools**
+
+=========================== ==================== ============================
+Name                        Output file          Format
+=========================== ==================== ============================
+xcms.findChromPeaks Merger  sampleMetadata.tsv   tabular
+=========================== ==================== ============================
+
+.. image:: xcms_merge_workflow.png
+
+-----------
+Input files
+-----------
+
+=========================== ==================================
+Parameter : num + label     Format
+=========================== ==================================
+1 : RData file              rdata.xcms.findchrompeaks
+--------------------------- ----------------------------------
+2 : RData file              rdata.xcms.findchrompeaks
+--------------------------- ----------------------------------
+N : RData file              rdata.xcms.findchrompeaks
+=========================== ==================================
+
+
+
+
+------------
+Output files
+------------
+
+Example of a sampleMetadata:
+
+=========================== ============
+sample_name                 class
+=========================== ============
+HU_neg_028                  bio
+--------------------------- ------------
+HU_neg_034                  bio
+--------------------------- ------------
+Blanc04                     blank
+--------------------------- ------------
+Blanc06                     blank
+--------------------------- ------------
+Blanc09                     blank
+=========================== ============
+
+---------------------------------------------------
+
+Changelog/News
+--------------
+
+**Version 3.0.0.0 - 09/10/2018**
+
+- NEW: a new tool to generate a sampleMetadata file you will be able to complete
+
+    ]]></help>
+
+    <expand macro="citation" />
+</tool>