Mercurial > repos > iuc > scanpy_inspect

changeset 18:d1cd8c147809 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
author iuc
date Thu, 19 Sep 2024 06:43:47 +0000
parents 18262103fa61
children
files inspect.xml macros.xml
diffstat 2 files changed, 72 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- a/inspect.xml	Sat Sep 14 12:45:03 2024 +0000
+++ b/inspect.xml	Thu Sep 19 06:43:47 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="scanpy_inspect" name="Scanpy Inspect and manipulate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="scanpy_inspect" name="Scanpy Inspect and manipulate" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <macros>
         <import>macros.xml</import>
         <xml name="params_score_genes">
@@ -146,7 +146,7 @@
     use_raw=$method.use_raw,
     #if str($method.groups) != '':
     #set $group=[x.strip() for x in str($method.groups).split(',')]
-    groups='$group',
+    groups=$group,
     #end if
     #if str($method.layer) != '':
     layer='$method.layer',
@@ -446,7 +446,7 @@
                                 <expand macro="fit_intercept"/>
                                 <expand macro="max_iter"/>
                                 <expand macro="multi_class"/>
-                            </when>                            
+                            </when>
                             <when value="newton-cg">
                                 <param name="penalty" type="boolean" truevalue="l2" falsevalue="None" checked="true" label="use l2 penalty?"/>
                                 <expand macro="fit_intercept"/>
@@ -560,8 +560,7 @@
         <expand macro="anndata_outputs"/>
     </outputs>
     <tests>
-
-        <!-- test 1 -->
+<!-- test 1 -->
         <test expect_num_outputs="2">
             <param name="adata" value="sparce_csr_matrix.h5ad"/>
             <conditional name="method">
@@ -614,7 +613,7 @@
                 </assert_contents>
             </output>
         </test>
-        
+
         <!-- test 3 -->
         <test expect_num_outputs="2">
             <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad"/>
@@ -851,10 +850,61 @@
                     <has_h5_keys keys="uns/rank_genes_groups"/>
                 </assert_contents>
             </output>
-        </test> 
+        </test>
 
         <!-- test 10 -->
         <test expect_num_outputs="2">
+            <param name="adata" value="krumsiek11.h5ad"/>
+            <conditional name="method">
+                <param name="method" value="tl.rank_genes_groups"/>
+                <param name="groupby" value="cell_type"/>
+                <param name="groups" value="Ery"/>
+                <conditional name="ref">
+                    <param name="rest" value="group_id"/>
+                    <param name="reference" value="Mk"/>
+                </conditional>
+                <param name="n_genes" value="100"/>
+                <conditional name="tl_rank_genes_groups_method">
+                    <param name="method" value="logreg"/>
+                    <conditional name="solver">
+                        <param name="solver" value="liblinear"/>
+                        <conditional name="penalty">
+                            <param name="penalty" value="l2"/>
+                            <param name="random_state" value="1"/>
+                        </conditional>
+                    </conditional>
+                </conditional>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true"/>
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="sc.tl.rank_genes_groups"/>
+                    <has_text_matching expression="groupby='cell_type'"/>
+                    <has_text_matching expression="use_raw=False"/>
+                    <has_text_matching expression="n_genes=100"/>
+                    <has_text_matching expression="method='logreg'"/>
+                    <has_text_matching expression="solver='liblinear'"/>
+                    <has_text_matching expression="penalty='l2'"/>
+                    <has_text_matching expression="dual=False"/>
+                    <has_text_matching expression="fit_intercept=True"/>
+                    <has_text_matching expression="intercept_scaling=1.0"/>
+                    <has_text_matching expression="tol=0.0001"/>
+                    <has_text_matching expression="C=1.0"/>
+                    <has_text_matching expression="groups=\['Ery'\]"/>
+                    <has_text_matching expression="reference='Mk'"/>
+                </assert_contents>
+            </output>
+            <output name="anndata_out" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="uns/rank_genes_groups"/>
+                </assert_contents>
+            </output>
+        </test>
+
+        <!-- test 11 -->
+        <test expect_num_outputs="2">
             <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad"/>
             <conditional name="method">
                 <param name="method" value="tl.marker_gene_overlap"/>
@@ -889,7 +939,7 @@
             </output>
         </test>
 
-        <!-- test 11 -->
+        <!-- test 12 -->
         <test expect_num_outputs="2">
             <param name="adata" value="krumsiek11.h5ad"/>
             <conditional name="method">
@@ -910,7 +960,7 @@
             </output>
         </test>
 
-        <!-- test 12 -->
+        <!-- test 13 -->
         <test expect_num_outputs="2">
             <param name="adata" value="krumsiek11.h5ad"/>
             <conditional name="method">
@@ -929,9 +979,10 @@
                 <assert_contents>
                     <has_h5_keys keys="var/mean,var/std"/>
                 </assert_contents>
-            </output>        </test>
+            </output>
+        </test>
 
-        <!-- test 13 -->
+        <!-- test 14 -->
         <test expect_num_outputs="2">
             <param name="adata" value="krumsiek11.h5ad"/>
             <conditional name="method">
@@ -955,7 +1006,7 @@
             </output>
         </test>
 
-        <!-- test 14 -->
+        <!-- test 15 -->
         <test expect_num_outputs="2">
             <param name="adata" value="random-randint.h5ad"/>
             <conditional name="method">
--- a/macros.xml	Sat Sep 14 12:45:03 2024 +0000
+++ b/macros.xml	Thu Sep 19 06:43:47 2024 +0000
@@ -9,7 +9,7 @@
             <requirement type="package" version="1.26.4">numpy</requirement>
             <requirement type="package" version="2.2.2">pandas</requirement>
             <requirement type="package" version="1.14.1">scipy</requirement>
-            <requirement type="package" version="0.14.2">statsmodels</requirement>           
+            <requirement type="package" version="0.14.2">statsmodels</requirement>
             <yield />
         </requirements>
     </xml>
@@ -29,8 +29,8 @@
             <citation type="doi">10.1093/gigascience/giaa102</citation>
         </citations>
     </xml>
-    
-    
+
+
     <!-- param macros -->
     <xml name="sanitize_query" token_validinitial="string.printable">
         <sanitizer>
@@ -45,7 +45,7 @@
                 <add value=","/>
             </valid>
         </sanitizer>
-    </xml>      
+    </xml>
     <xml name="inputs_anndata">
         <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
     </xml>
@@ -61,7 +61,7 @@
         <data name="hidden_output" format="txt" label="Log file" >
             <filter>advanced_common['show_log']</filter>
         </data>
-    </xml>    
+    </xml>
     <xml name="param_use_rep">
         <param argument="use_rep" type="text" value="" optional="true" label="Use the indicated representation" help="If not set, the representation is chosen automatically: for n_vars below 50, X is used, otherwise X_pca (uns) is used. If X_pca is not present, it's computed with default parameter">
                 <expand macro="sanitize_query"/>
@@ -546,7 +546,7 @@
     <!-- param macros -->
 
 
-    
+
     <!-- command macros -->
     <xml name="version_command">
         <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command>
@@ -936,7 +936,7 @@
 #end if
     ]]>
     </token>
-    
+
     <xml name="params_seaborn_violinplot">
         <section name="seaborn_violinplot" title="Parameters for seaborn.violinplot">
             <param argument="bw_method" type="select" label="Name of a reference rule when computing the kernel bandwidth">
@@ -969,7 +969,7 @@
     #end if
     saturation=$method.seaborn_violinplot.saturation,
     ]]></token>
-   
+
     <xml name="param_color">
         <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either '.obs' or '.var'">
             <expand macro="sanitize_query"/>
@@ -1017,7 +1017,7 @@
 #end if
     ]]>
     </token>
-    
+
     <xml name="param_legend_fontsize">
         <param argument="legend_fontsize" type="integer" optional="true" value="" label="Legend font size"/>
     </xml>