diff macros.xml @ 0:b6b051e7a5ef draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Mar 05 10:08:14 2018 -0500
@@ -0,0 +1,90 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+           <requirement type="package" version="1.4.5" >bioconductor-mspurity</requirement>
+           <requirement type="package" version="1.4.4" >r-optparse</requirement>
+            <yield />
+        </requirements>
+
+    </xml>
+
+    <xml name="offsets">
+            <param name="minoffset" type="float" label="minoffset" value="0.5"
+                    help="Offset to the 'left' for the precursor range e.g. if precursor of interest is
+                    100.0 then the range would be from 999.5 to 100.0"/>
+        <param name="maxoffset" type="float" label="maxoffset" value="0.5"
+                    help="Offset to the 'right' for the precursor range  e.g. if precursor of interest is
+                    100.0 then the range would be from 100.0 to 100.5"/>
+    </xml>
+    <xml name="general_params">
+
+        <param name="ilim" type="float" label="ilim" value="0.05"
+                    help="All peaks less than this percentage of the target peak will be removed
+                    from the purity calculation, default is 5\% (0.05)"/>
+
+        <param name="iw_norm" type="select" label="Normalisation for isolation efficiency">
+                <option value="gauss" >Gaussian</option>
+                <option value="rcosine" >Raised cosine</option>
+                <option value="QE5"> Calculated from Q-Exactive for +/- 0.5 Da windows </option>
+                <option value="none" selected="true" >No normalisation</option>
+        </param>
+
+        <conditional name="isotopes">
+            <param name="isotopes" type="select" label="Handling of isotopic peaks" >
+                <option value="keep" >Keep isotopes in precursor ion purity calculation</option>
+                <option value="exclude_default" selected="true" >Exclude C12/C13 isotopes in precursor ion purity calculation</option>
+                <option value="user" >Exclude a user supplied list of isotopes in purity calculation</option>
+            </param>
+            <when value="keep">
+            </when>
+            <when value="exclude_default">
+            </when>
+            <when value="user">
+                <param name="im" type="data" format="tabular" label="Isotope matrix" help="
+                 tabular file composing of columns:
+                  ['isotope_id', 'mass diff', 'abundance of isotope', 'ppm tol for mz', 'abundance buffer',
+                                  'charge', 'relative atomic mass (int)', 'xflag'].
+                The xflag indicates if the larger (mass) isotope is the most abundant or less abundant.
+                e.g. for c12 to c13, the c13 is less abundant so we flag as 1 for Li6 to Li7, the Li7 is more abundant
+                so we would flag as 0.
+                Example row: For C13 isotope (single charge) the row could be [1, 1.003355, 1.07, 4, 0.1, 1, 12, 1]"/>
+            </when>
+        </conditional>
+    </xml>
+
+
+
+
+
+
+
+    <xml name="fileload">
+            <conditional name="file_load_conditional">
+                <param name="file_load_select" type="select" label="Resubmit your dataset"
+                       help="Use only if you get a message which say that your original dataset or
+                                dataset collection can not be found the server." >
+                    <option value="no" >no need</option>
+                    <option value="yes" >yes</option>
+                </param>
+                <when value="no">
+                </when>
+                <when value="yes">
+                    <param name="input" type="data_collection" collection_type="list"  format="mzxml,mzml,mzdata,netcdf"
+                           multiple="true" label="File(s) from your history containing your chromatograms"
+                           help="Select the dataset collection containing the files that were used
+                                 for processing" />
+                </when>
+        </conditional>
+    </xml>
+
+
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1021/acs.analchem.6b04358</citation>
+            <yield />
+        </citations>
+    </xml>
+
+</macros>