Remove input scan format conditional.

galaxyproteomics · Jun 26, 2024 · 97718b1 · 97718b1
1 parent ef0f93e
commit 97718b1
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Showing 3 changed files with 5 additions and 28 deletions.
diff --git a/tools/fragpipe/fragpipe.xml b/tools/fragpipe/fragpipe.xml
@@ -158,7 +158,6 @@
 
     <tests>
       <test expect_num_outputs="11">
-        <param name="scanformat" value="mzML"/>
         <param name="inputs" value="default/test1.mzML,default/test2.mzML" ftype="mzml"/>
         <param name="database_name" value="default/test.fasta" ftype="fasta"/>
         <param name="manifest" value="default/test.manifest" ftype="tabular"/>
@@ -208,7 +207,6 @@
         </output_collection>
       </test>
       <test expect_num_outputs="11">
-        <param name="scanformat" value="mzML"/>
         <param name="inputs" value="tmt11/test1.mzML,tmt11/test2.mzML" ftype="mzml"/>
         <param name="database_name" value="tmt11/test.fasta" ftype="fasta"/>
         <param name="manifest" value="tmt11/test.manifest" ftype="tabular"/>

diff --git a/tools/fragpipe/macros.xml b/tools/fragpipe/macros.xml
@@ -20,22 +20,10 @@
       name, experiment, bioreplicate, data type
     -->
     <xml name="samples">
-        <conditional name="scan">
-            <param name="scanformat" type="select" label="Scan files format">
-                <option value="mzML">mzML</option>
-                <option value="mzXML">mzXML</option>
-                <option value="raw">Thermo.raw</option>
-            </param>
-            <when value="mzML">
-                <expand macro="scan_inputs" scanformat="mzml"/>
-            </when>
-            <when value="mzXML">
-                <expand macro="scan_inputs" scanformat="mzxml"/>
-            </when>
-            <when value="raw">
-                <expand macro="scan_inputs" scanformat="thermo.raw"/>
-            </when>
-        </conditional>
+        <param name="inputs" type="data" format="mzML,mzXML,Thermo.raw" multiple="true" label="Proteomics Spectrum files"  help="All input scan files must of a matching format: mzML, mzXML, or Thermo.raw"/>
+        <param name="input_prefix" type="text" value="" optional="true" label="File name prefix" help="Names inputs: prefix_rep#.mzXML Leave blank to use History names of inputs">
+              <validator type="regex" message="">[a-zA-Z][a-zA-Z0-9_-]*</validator>
+        </param>
         <param name="manifest" type="data" format="tabular" label="Manifest file" help="TSV file with entries for each input scan file: Name (name of input Galaxy history item), Experiment (empty, alphanumeric, or _), Bioreplicate (empty or integer), Data type (DDA, DIA, GPF-DIA, DIA-Quant, or DIA-lib)"/>
     </xml>
 
@@ -58,7 +46,7 @@
 
     sed "s/^/\$CWD\/scans\//" $manifest > fp.manifest &&
 
-    #for $sf in $scan.inputs
+    #for $sf in $inputs
       #set $i_name = $ln_name($sf)
       ln -s '$sf' 'scans/${i_name}' &&
     #end for

diff --git a/tools/fragpipe/msfragger_macros.xml b/tools/fragpipe/msfragger_macros.xml
@@ -34,15 +34,6 @@
 #set $db_name = None
     </token>
 
-    <!-- Input scan files -->
-    <xml name="scan_inputs" token_scanformat="thermo.raw,mzml,imzml,mzxmli,mgf">
-        <param name="inputs" type="data" format="@SCANFORMAT@" multiple="true" label="Proteomics Spectrum files"  help="Thermo RAW, mzML, mzXML, MGF formats"/>
-        <param name="input_prefix" type="text" value="" optional="true" label="File name prefix" help="Names inputs: prefix_rep#.mzXML Leave blank to use History names of inputs">
-              <validator type="regex" message="">[a-zA-Z][a-zA-Z0-9_-]*</validator>
-        </param>
-    </xml>
-
-
     <!-- The following xml elements define the parameters for each given workflow -->
     <xml name="msfragger_default">
         <expand macro="search_tolerances"/>