diff macros.xml @ 15:f5d54dc64697 draft

"planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 91a0182476a7fc26be7bef1677790518c4e88348-dirty"

--- a/macros.xml	Mon Dec 09 10:37:59 2019 +0000
+++ b/macros.xml	Mon Dec 16 13:12:48 2019 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
-    <token name="@WRAPPER_VERSION@">3.3.1</token>
+    <token name="@WRAPPER_VERSION@">2.1.4</token>
     <token name="@USE_RANGE@">
         #if $use_range.select_use_range == "yes_use_range":
             --range $range_min:$range_max
@@ -15,25 +15,6 @@
         <version_command>@BINARY@ --version</version_command>
     </xml>
 
-    <token name="@CHROMOSOME_LIST@">
-        #if $chromosome_list:
-            #set $chromosomes = []
-            #for $chrom in $chromosome_list:
-                #silent $chromosomes.append("'%s'" % $chrom.chromosomes)
-            #end for
-            #set $chromosome_string = ' '.join($chromosomes)
-            --chromosomes $chromosome_string
-        #end if
-    </token>
-
-    <xml name="chromosome_list">
-        <repeat name="chromosome_list" min="0" title="Chromosomes to include" help="Chromosomes to include in the analysis. If not set, all chromosomes are included.">
-            <param argument="--chromosomes" type="text" value="" >
-                <validator type="empty_field" />
-            </param>
-        </repeat>
-    </xml>
-
     <xml name="citations">
         <citations>
             <citation type="doi">10.5281/zenodo.1133705</citation>
@@ -133,7 +114,6 @@
             <option value="brg">brg</option>
             <option value="jet">jet</option>
             <option value="afmhot">afmhot</option>
-            <option value="plasma">plasma</option>
             <option value="Accent_r">Accent reversed</option>
             <option value="Spectral_r">Spectral reversed</option>
             <option value="Set1_r">Set1 reversed</option>
@@ -203,10 +183,10 @@
             <option value="brg_r">brg reversed</option>
             <option value="jet_r">jet reversed</option>
             <option value="afmhot_r">afmhot reversed</option>
-            <option value="plasma_r">plasma reversed</option>
         </param>
     </xml>
 
+
     <xml name="multiple_input_matrices">
         <repeat name="input_files" title="Hi-C Matrix files" min="2">
             <param name="matrix" type="data" format="h5,cool"
@@ -222,22 +202,19 @@
         #set $matrices = []
         #set $mlabels = []
         #for $counter, $i in enumerate($input_files):
-            ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext'; 
-            #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter,  $i.matrix.ext))
+            ln -s $i.matrix #echo str($counter)+'_matrix'#;
+            #silent $matrices.append( '%s_matrix' % $counter )
 
             #if str($i.mlabel.value) != "":
-                #set $mlabels += ['\'%s\'' % ($i.mlabel.value)]
+                #set $mlabels += ['"%s"' % ($i.mlabel.value)]
             #else
-                #set $mlabels += ['\'%s\'' % ($i.matrix.name)]
+                #set $mlabels += ['"%s"' % ($i.matrix.name)]
             #end if
         #end for
         #set $mlabels = ' '.join($mlabels)
         #set $matrices = ' '.join($matrices)
     </token>
 
-    <token name="@ESCAPE_IDENTIFIER_FILE@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))]]></token>
-    <token name="@ESCAPE_IDENTIFIER_MATRIX@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($matrix.element_identifier))]]></token>
-    <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))]]></token>
 
     <xml name="region">
         <param name="region" type="text" label="Region of the genome to limit the operation"
@@ -353,96 +330,6 @@
         <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
             label="Matricies to compute on" multiple="true"/>
     </xml>
-
-    
-
-    <xml name='convertFormat_single_macro'>
-        <conditional name="inputFormat_conditional">
-            <param name="inputFormat_selector" type="select" label="Choose input file type">
-                <option value="optionCool" selected="True">cool</option>
-                <option value="optionH5">h5</option>
-                <!-- <option value="optionHic">hic</option> -->
-                <option value="optionHomer">Homer</option>
-                <option value="optionHicpro">HiCPro</option>
-            </param>
-            <when value="optionCool">
-                <expand macro='matrix_h5_cooler_macro' />
-                <param name='correctionName' type='text' label='Correction factors column name'/>
-                <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication'/>
-                <param name='chromosome' type='text' label='Load only one chromosome'/>
-                <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/>
-
-            </when>
-            <when value="optionH5">
-                <expand macro='matrix_h5_cooler_macro' />
-            </when>
-            <!-- <when value="optionHic">
-                <param name='matrixHic' type='data' format='binary' label='.hic matrix'/>
-                <param name='resolutions' type='text' label='List of resolutions'/>
-            </when> --> 
-
-            <when value="optionHomer">
-                <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix'/>
-            </when>
-
-            <when value="optionHicpro">
-                <param name='matrixHicpro' type='data' format='txt' label='.hic matrix'/>
-                <param name='bedHicpro' type='data' format='bed' label='HicPro bed file'/>
-            </when>
-        </conditional>
-    </xml>
-
-    <xml name='convertFormat_multiple_macro'>
-        <conditional name="inputFormat_conditional">
-            <param name="inputFormat_selector" type="select" label="Choose input file type">
-                <option value="optionCool" selected="True">cool</option>
-                <option value="optionH5">h5</option>
-                <option value="optionHomer">Homer</option>
-                <option value="optionHicpro">HiCPro</option>
-            </param>
-            <when value="optionCool">
-                <expand macro='matrix_h5_cooler_multiple_macro' />
-                <param name='correctionName' type='text' label='Correction factors column name'/>
-                <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication'/>
-                <param name='chromosome' type='text' label='Load only one chromosome'/>
-                <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/>
-
-            </when>
-            <when value="optionH5">
-                <expand macro='matrix_h5_cooler_multiple_macro' />
-            </when>
-           
-            <when value="optionHomer">
-                <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' multiple="true"/>
-            </when>
-
-            <when value="optionHicpro">
-                <param name='matrixHicpro' type='data' format='txt' label='.hic matrix' multiple="true"/>
-                <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' multiple="true"/>
-            </when>
-        </conditional>
-    </xml>
-    <xml name='convertFormat_single_output_macro'>
-        <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> -->
-
-        <conditional name="outputFormat_conditional">
-            <param name="outputFormat_selector" type="select" label="Choose output file type">
-                <option value="cool" selected="True">cool</option>
-                <option value="h5">h5</option>
-                <option value="homer">Homer</option>
-                <option value="ginteractions">ginteractions</option>
-
-            </param>
-            <when value="cool">
-                <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue=""   label='Store applied correction factors in column count'/>
-                <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue=""  label='Enforce integer for count column'/>
-            </when>
-            <when value='h5'/>
-            <when value='homer'/>
-            <when value='ginteractions'/>
-
-        </conditional>
-    </xml>
     <token name="@REFERENCES@">
 
 .. class:: infomark