diff remove_confounders.xml @ 7:215733a383f2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"

--- a/remove_confounders.xml	Thu Feb 20 08:24:15 2020 -0500
+++ b/remove_confounders.xml	Wed May 20 16:07:23 2020 -0400
@@ -72,19 +72,27 @@
                 <option value="pp.combat">Correct batch effects with ComBat function, using 'pp.combat'</option>
             </param>
             <when value="pp.regress_out">
-                <param argument="keys" type="text" value="" label="Keys for observation annotation on which to regress on" help="Keys separated by a comma"/>
+                <param argument="keys" type="text" value="" label="Keys for observation annotation on which to regress on" help="Keys separated by a comma">
+                    <expand macro="sanitize_query" />
+                </param>
             </when>
             <when value="pp.mnn_correct">
                 <param name="extra_adata" type="data" multiple="true" optional="true" format="h5ad" label="Extra annotated data matrix" help="They should have same number of variables."/>
-                <param argument="var_subset" type="text" value="" optional="true" label="The subset of vars to be used when performing MNN correction" help="List of comma-separated key from '.var_names'. If not set, all vars are used"/>
-                <param argument="batch_key" type="text" value="batch" label="Batch key for the concatenate"/>
+                <param argument="var_subset" type="text" value="" optional="true" label="The subset of vars to be used when performing MNN correction" help="List of comma-separated key from '.var_names'. If not set, all vars are used">
+                    <expand macro="sanitize_query" />
+                </param>
+                <param argument="batch_key" type="text" value="batch" label="Batch key for the concatenate">
+                    <expand macro="sanitize_query" />
+                </param>
                 <param name="index_unique" type="select" label="Separator to join the existing index names with the batch category" help="Leave it empty to keep existing indices">
                     <option value="-">-</option>
                     <option value="_">_</option>
                     <option value=" "> </option>
                     <option value="/">/</option>
                 </param>
-                <param argument="batch_categories" type="text" value="" optional="true" label="Batch categories for the concatenate" help="List of comma-separated key"/>
+                <param argument="batch_categories" type="text" value="" optional="true" label="Batch categories for the concatenate" help="List of comma-separated key">
+                    <expand macro="sanitize_query" />
+                </param>
                 <param argument="k" type="integer" value="20" label="Number of mutual nearest neighbors"/>
                 <param argument="sigma" type="float" value="1" label="The bandwidth of the Gaussian smoothing kernel used to compute the correction vectors"/>
                 <param argument="cos_norm_in" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Should cosine normalization be performed on the input data prior to calculating distances between cells?"/>
@@ -92,7 +100,9 @@
                 <param argument="svd_dim" type="integer" value="" optional="true" label="Number of dimensions to use for summarizing biological substructure within each batch" help="If not set, biological components will not be removed from the correction vectors."/>
                 <param argument="var_adj" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Adjust variance of the correction vectors?" help="This step takes most computing time."/>
                 <param argument="compute_angle" type="boolean" truevalue="True" falsevalue="False" checked="false" label="compute the angle between each cell’s correction vector and the biological subspace of the reference batch?"/>
-                <param argument="mnn_order" type="text" value="" optional="true" label="The order in which batches are to be corrected" help="List of comma-separated key. If not set, datas are corrected sequentially"/>
+                <param argument="mnn_order" type="text" value="" optional="true" label="The order in which batches are to be corrected" help="List of comma-separated key. If not set, datas are corrected sequentially">
+                    <expand macro="sanitize_query" />
+                </param>
                 <param name="svd_mode" type="select" label="SVD mode">
                     <option value="svd">svd: SVD using a non-randomized SVD-via-ID algorithm</option>
                     <option value="rsvd" selected="true">rsvd: SVD using a randomized SVD-via-ID algorithm</option>
@@ -100,7 +110,9 @@
                 </param>
             </when>
             <when value="pp.combat">
-                <param argument="key" type="text" value="batch" label="Key to a categorical annotation from adata.obs that will be used for batch effect removal"/>
+                <param argument="key" type="text" value="batch" label="Key to a categorical annotation from adata.obs that will be used for batch effect removal">
+                    <expand macro="sanitize_query" />
+                </param>
             </when>
         </conditional>
         <expand macro="inputs_common_advanced"/>