Mercurial > repos > iuc > scanpy_cluster_reduce_dimension

changeset 6:77b91b9bdf52 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
author iuc
date Thu, 20 Feb 2020 08:23:29 -0500
parents 6f2d2c7f77ee
children b2df381a6004
files cluster_reduce_dimension.xml macros.xml
diffstat 2 files changed, 163 insertions(+), 95 deletions(-) [+]
line wrap: on
line diff
--- a/cluster_reduce_dimension.xml	Mon Feb 10 05:27:02 2020 -0500
+++ b/cluster_reduce_dimension.xml	Thu Feb 20 08:23:29 2020 -0500
@@ -276,13 +276,14 @@
                 </param>
             </when>
         </conditional>            
+        <expand macro="inputs_common_advanced"/>
     </inputs>
     <outputs>
         <expand macro="anndata_outputs"/>
     </outputs>
     <tests>
         <test>
-            <!-- test 1 -->
+            <!-- test 0 -->
             <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
             <conditional name="method">
                 <param name="method" value="tl.louvain"/>
@@ -295,20 +296,25 @@
                 <param name="directed" value="true"/>
                 <param name="use_weights" value="false"/>
             </conditional>
-            <assert_stdout>
-                <has_text_matching expression="sc.tl.louvain"/>
-                <has_text_matching expression="adata=adata"/>
-                <has_text_matching expression="flavor = 'vtraag'"/>
-                <has_text_matching expression="resolution=1.0"/>
-                <has_text_matching expression="random_state=10"/>
-                <has_text_matching expression="key_added='louvain'"/>
-                <has_text_matching expression="directed=True"/>
-                <has_text_matching expression="use_weights=False"/>
-            </assert_stdout>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="sc.tl.louvain"/>
+                    <has_text_matching expression="adata=adata"/>
+                    <has_text_matching expression="flavor = 'vtraag'"/>
+                    <has_text_matching expression="resolution=1.0"/>
+                    <has_text_matching expression="random_state=10"/>
+                    <has_text_matching expression="key_added='louvain'"/>
+                    <has_text_matching expression="directed=True"/>
+                    <has_text_matching expression="use_weights=False"/>
+                </assert_contents>
+            </output>
             <output name="anndata_out" file="tl.louvain.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
         <test>
-            <!-- test 2 -->
+            <!-- test 1 -->
             <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
             <conditional name="method">
                 <param name="method" value="tl.leiden"/>
@@ -318,18 +324,23 @@
                 <param name="use_weights" value="false"/>
                 <param name="n_iterations" value="-1"/>
             </conditional>
-            <assert_stdout>
-                <has_text_matching expression="sc.tl.leiden"/>
-                <has_text_matching expression="resolution=1"/>
-                <has_text_matching expression="random_state=10"/>
-                <has_text_matching expression="key_added='leiden'"/>
-                <has_text_matching expression="use_weights=False"/>
-                <has_text_matching expression="n_iterations=-1"/>
-            </assert_stdout>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="sc.tl.leiden"/>
+                    <has_text_matching expression="resolution=1"/>
+                    <has_text_matching expression="random_state=10"/>
+                    <has_text_matching expression="key_added='leiden'"/>
+                    <has_text_matching expression="use_weights=False"/>
+                    <has_text_matching expression="n_iterations=-1"/>
+                </assert_contents>
+            </output>
             <output name="anndata_out" file="tl.leiden.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
         <test>
-            <!-- test 2 -->
+            <!-- test 1 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="pp.pca"/>
@@ -343,17 +354,22 @@
                 </conditional>
                 <param name="use_highly_variable" value="false"/>
             </conditional>
-            <assert_stdout>
-                <has_text_matching expression="sc.pp.pca"/>
-                <has_text_matching expression="n_comps=50"/>
-                <has_text_matching expression="dtype='float32'"/>
-                <has_text_matching expression="copy=False"/>
-                <has_text_matching expression="chunked=False"/>
-                <has_text_matching expression="zero_center=True"/>
-                <has_text_matching expression="svd_solver='auto'"/>
-                <has_text_matching expression="random_state=0"/>
-                <has_text_matching expression="use_highly_variable=False"/>
-            </assert_stdout>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="sc.pp.pca"/>
+                    <has_text_matching expression="n_comps=50"/>
+                    <has_text_matching expression="dtype='float32'"/>
+                    <has_text_matching expression="copy=False"/>
+                    <has_text_matching expression="chunked=False"/>
+                    <has_text_matching expression="zero_center=True"/>
+                    <has_text_matching expression="svd_solver='auto'"/>
+                    <has_text_matching expression="random_state=0"/>
+                    <has_text_matching expression="use_highly_variable=False"/>
+                </assert_contents>
+            </output>
             <output name="anndata_out" file="pp.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
         <!--<test>
@@ -383,7 +399,7 @@
         </test>
         -->
         <test>
-            <!-- test 3 -->
+            <!-- test 2 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="tl.pca"/>
@@ -397,33 +413,43 @@
                 </conditional>
                 <param name="use_highly_variable" value="false"/>
             </conditional>
-            <assert_stdout>
-                <has_text_matching expression="sc.tl.pca"/>
-                <has_text_matching expression="n_comps=50"/>
-                <has_text_matching expression="dtype='float32'"/>
-                <has_text_matching expression="copy=False"/>
-                <has_text_matching expression="chunked=False"/>
-                <has_text_matching expression="zero_center=True"/>
-                <has_text_matching expression="svd_solver='auto'"/>
-                <has_text_matching expression="use_highly_variable=False"/>
-            </assert_stdout>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="sc.tl.pca"/>
+                    <has_text_matching expression="n_comps=50"/>
+                    <has_text_matching expression="dtype='float32'"/>
+                    <has_text_matching expression="copy=False"/>
+                    <has_text_matching expression="chunked=False"/>
+                    <has_text_matching expression="zero_center=True"/>
+                    <has_text_matching expression="svd_solver='auto'"/>
+                    <has_text_matching expression="use_highly_variable=False"/>
+                </assert_contents>
+            </output>
             <output name="anndata_out" file="tl.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
         <test>
-            <!-- test 4 -->
+            <!-- test 3 -->
             <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
             <conditional name="method">
                 <param name="method" value="tl.diffmap"/>
                 <param name="n_comps" value="15"/>
             </conditional>
-            <assert_stdout>
-                <has_text_matching expression="sc.tl.diffmap"/>
-                <has_text_matching expression="n_comps=15"/>
-            </assert_stdout>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="sc.tl.diffmap"/>
+                    <has_text_matching expression="n_comps=15"/>
+                </assert_contents>
+            </output>
             <output name="anndata_out" file="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
         <test>
-            <!-- test 5 -->
+            <!-- test 4 -->
             <param name="adata" value="krumsiek11.h5ad" />
             <conditional name="method">
                 <param name="method" value="tl.tsne"/>
@@ -434,19 +460,24 @@
                 <param name="random_state" value="0"/>
                 <param name="use_fast_tsne" value="true"/>
             </conditional>
-            <assert_stdout>
-                <has_text_matching expression="sc.tl.tsne"/>
-                <has_text_matching expression="n_pcs=10"/>
-                <has_text_matching expression="perplexity=30.0"/>
-                <has_text_matching expression="early_exaggeration=12.0"/>
-                <has_text_matching expression="learning_rate=1000.0"/>
-                <has_text_matching expression="random_state=0"/>
-                <has_text_matching expression="use_fast_tsne=True"/>
-            </assert_stdout>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="sc.tl.tsne"/>
+                    <has_text_matching expression="n_pcs=10"/>
+                    <has_text_matching expression="perplexity=30.0"/>
+                    <has_text_matching expression="early_exaggeration=12.0"/>
+                    <has_text_matching expression="learning_rate=1000.0"/>
+                    <has_text_matching expression="random_state=0"/>
+                    <has_text_matching expression="use_fast_tsne=True"/>
+                </assert_contents>
+            </output>
             <output name="anndata_out" file="tl.tsne.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
         <test>
-            <!-- test 6 -->
+            <!-- test 5 -->
             <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
             <conditional name="method">
                 <param name="method" value="tl.umap"/>
@@ -460,18 +491,23 @@
                 <param name="init_pos" value="spectral"/>
                 <param name="random_state" value="0"/>
             </conditional>
-            <assert_stdout>
-                <has_text_matching expression="sc.tl.umap"/>
-                <has_text_matching expression="min_dist=0.5"/>
-                <has_text_matching expression="spread=1.0"/>
-                <has_text_matching expression="n_components=2"/>
-                <has_text_matching expression="maxiter=2"/>
-                <has_text_matching expression="alpha=1.0"/>
-                <has_text_matching expression="gamma=1.0"/>
-                <has_text_matching expression="negative_sample_rate=5"/>
-                <has_text_matching expression="init_pos='spectral'"/>
-                <has_text_matching expression="random_state=0"/>
-            </assert_stdout>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="sc.tl.umap"/>
+                    <has_text_matching expression="min_dist=0.5"/>
+                    <has_text_matching expression="spread=1.0"/>
+                    <has_text_matching expression="n_components=2"/>
+                    <has_text_matching expression="maxiter=2"/>
+                    <has_text_matching expression="alpha=1.0"/>
+                    <has_text_matching expression="gamma=1.0"/>
+                    <has_text_matching expression="negative_sample_rate=5"/>
+                    <has_text_matching expression="init_pos='spectral'"/>
+                    <has_text_matching expression="random_state=0"/>
+                </assert_contents>
+            </output>
             <output name="anndata_out" file="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size">
                 <assert_contents>
                     <has_h5_keys keys="X, obs, obsm, uns, var" />
@@ -479,22 +515,27 @@
             </output>
         </test>
         <test>
-            <!-- test 7 -->
+            <!-- test 6 -->
             <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
             <conditional name="method">
                 <param name="method" value="tl.draw_graph"/>
                 <param name="layout" value="fa"/>
                 <param name="random_state" value="0"/>
             </conditional>
-            <assert_stdout>
-                <has_text_matching expression="sc.tl.draw_graph"/>
-                <has_text_matching expression="layout='fa'"/>
-                <has_text_matching expression="random_state=0"/>
-            </assert_stdout>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="sc.tl.draw_graph"/>
+                    <has_text_matching expression="layout='fa'"/>
+                    <has_text_matching expression="random_state=0"/>
+                </assert_contents>
+            </output>
             <output name="anndata_out" file="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
         <test>
-            <!-- test 8 -->
+            <!-- test 7 -->
             <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
             <conditional name="method">
                 <param name="method" value="tl.paga"/>
@@ -502,16 +543,21 @@
                 <param name="use_rna_velocity" value="False"/>
                 <param name="model" value="v1.2"/>
             </conditional>
-            <assert_stdout>
-                <has_text_matching expression="sc.tl.paga"/>
-                <has_text_matching expression="groups='paul15_clusters'"/>
-                <has_text_matching expression="use_rna_velocity=False"/>
-                <has_text_matching expression="model='v1.2'"/>
-            </assert_stdout>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="sc.tl.paga"/>
+                    <has_text_matching expression="groups='paul15_clusters'"/>
+                    <has_text_matching expression="use_rna_velocity=False"/>
+                    <has_text_matching expression="model='v1.2'"/>
+                </assert_contents>
+            </output>
             <output name="anndata_out" file="tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
         <test>
-            <!-- test 9 -->
+            <!-- test 8 -->
             <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
             <conditional name="method">
                 <param name="method" value="tl.dpt"/>
@@ -520,13 +566,18 @@
                 <param name="min_group_size" value="0.01"/>
                 <param name="allow_kendall_tau_shift" value="True"/>
             </conditional>
-            <assert_stdout>
-                <has_text_matching expression="sc.tl.dpt"/>
-                <has_text_matching expression="n_dcs=15"/>
-                <has_text_matching expression="n_branchings=1"/>
-                <has_text_matching expression="min_group_size=0.01"/>
-                <has_text_matching expression="allow_kendall_tau_shift=True"/>
-            </assert_stdout>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="sc.tl.dpt"/>
+                    <has_text_matching expression="n_dcs=15"/>
+                    <has_text_matching expression="n_branchings=1"/>
+                    <has_text_matching expression="min_group_size=0.01"/>
+                    <has_text_matching expression="allow_kendall_tau_shift=True"/>
+                </assert_contents>
+            </output>
             <output name="anndata_out" file="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
     </tests>
--- a/macros.xml	Mon Feb 10 05:27:02 2020 -0500
+++ b/macros.xml	Thu Feb 20 08:23:29 2020 -0500
@@ -21,12 +21,17 @@
     </xml>
     <token name="@CMD@"><![CDATA[
 cp '$adata' 'anndata.h5ad' &&
-cat '$script_file' &&
-python '$script_file' &&
-ls .
+cat '$script_file' > '$hidden_output' &&
+python '$script_file' >> '$hidden_output' &&
+ls . >> '$hidden_output' &&
+touch 'anndata_info.txt' &&
+cat 'anndata_info.txt' @CMD_prettify_stdout@
     ]]>
     </token>
     <token name="@CMD_imports@"><![CDATA[
+import sys
+sys.stderr = open('$hidden_output', 'a')
+
 import scanpy as sc
 import pandas as pd
 import numpy as np
@@ -39,13 +44,25 @@
 adata = sc.read('anndata.h5ad')
 ]]>
     </token>
+    <xml name="inputs_common_advanced">
+        <section name="advanced_common" title="Advanced Options" expanded="false">
+            <param name="show_log" type="boolean" checked="false" label="Output Log?" />
+        </section>
+    </xml>
     <xml name="anndata_outputs">
         <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/>
+        <data name="hidden_output" format="txt" label="Log file" >
+            <filter>advanced_common['show_log']</filter>
+        </data>
     </xml>
     <token name="@CMD_anndata_write_outputs@"><![CDATA[
 adata.write('anndata.h5ad')
+with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
+    print(adata, file=ainfo)
 ]]>
     </token>
+    <token name="@CMD_prettify_stdout@"><![CDATA[ | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g"  | sed -r 's|^\s*(.*):\s(.*)|[\1]\n-    \2|g' | sed 's|, |\n-    |g'
+    ]]></token>
     <xml name="svd_solver">
         <param name="svd_solver" type="select" label="SVD solver to use" help="">
             <option value="auto">Automatically chosen depending on the size of the problem</option>