diff normalize.xml @ 3:d7ea9b5e6df1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"

--- a/normalize.xml	Thu Dec 05 07:12:40 2019 -0500
+++ b/normalize.xml	Thu Dec 12 09:27:00 2019 -0500
@@ -23,11 +23,15 @@
     #if $method.exclude_highly_expressed.exclude_highly_expressed == "True"
     max_fraction=$method.exclude_highly_expressed.max_fraction,
     #end if
+    #if str($method.key_added) != ''
     key_added='$method.key_added',
-    #if str($method.layers) != 'all'
+    #end if
+    #if str($method.layers) != ''
+        #if str($method.layers) != 'all'
     layers[str(x.strip()) for x in str($method.layers).split(',')],
-    #else
+        #else
     layers='$method.layers',
+        #end if
     #end if
     #if str($method.layer_norm) != "None"
         layer_norm='$method.layer_norm',
@@ -70,10 +74,10 @@
         <expand macro="inputs_anndata"/>
         <conditional name="method">
             <param argument="method" type="select" label="Method used for normalization">
-                <option value="pp.normalize_total">Normalize counts per cell, using `pp.normalize_total`</option>
-                <option value="pp.recipe_zheng17">Normalization and filtering as of Zheng et al. (2017), using `pp.recipe_zheng17`</option>
-                <option value="pp.recipe_weinreb17">Normalization and filtering as of Weinreb et al (2017), using `pp.recipe_weinreb17`</option>
-                <option value="pp.recipe_seurat">Normalization and filtering as of Seurat et al (2015), using `pp.recipe_seurat`</option>
+                <option value="pp.normalize_total">Normalize counts per cell, using 'pp.normalize_total'</option>
+                <option value="pp.recipe_zheng17">Normalization and filtering as of Zheng et al. (2017), using 'pp.recipe_zheng17'</option>
+                <option value="pp.recipe_weinreb17">Normalization and filtering as of Weinreb et al (2017), using 'pp.recipe_weinreb17'</option>
+                <option value="pp.recipe_seurat">Normalization and filtering as of Seurat et al (2015), using 'pp.recipe_seurat'</option>
             </param>
             <when value="pp.normalize_total">
                 <param argument="target_sum" type="float" value="" optional="true" label="Target sum" help="If not provided, after normalization, each observation (cell) has a total count equal to the median of the total counts (cells) before normalization."/>
@@ -87,8 +91,8 @@
                     </when>
                     <when value="False"/>
                 </conditional>
-                <param argument="key_added" type="text" value="n_counts" label="Name of the field in `adata.obs` where the normalization factor is stored" help=""/>
-                <param argument="layers" type="text" value="all" label="List of layers to normalize" help="'All' will normalize all layers. The list should be comma-separated."/>
+                <param argument="key_added" type="text" value="" optional="true" label="Name of the field in 'adata.obs' where the normalization factor is stored" help=""/>
+                <param argument="layers" type="text" value="" optional="true" label="List of layers to normalize" help="'All' will normalize all layers. The list should be comma-separated."/>
                 <param argument="layer_norm" type="select" label="How to normalize layers?">
                     <option value="None">None: after normalization, for each layer in layers each cell has a total count equal to the median of the median of the total counts (cells) before normalization of the layer.</option>
                     <option value="after">After: for each layer in layers each cell has a total count equal to target_sum.</option>