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Fix scanpy by using profile #2704

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Dec 5, 2019
Merged

Fix scanpy by using profile #2704

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391b091
Fix scanpy by using profile
mvdbeek Nov 29, 2019
8573e8a
Bump scanpy to 1.4.4.post1 which includes louvain depencency
mvdbeek Nov 30, 2019
07c6c3b
Add louvain dependency to scanpy/cluster_reduce_dimension.xml
mvdbeek Dec 2, 2019
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6 changes: 4 additions & 2 deletions tools/scanpy/cluster_reduce_dimension.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="scanpy_cluster_reduce_dimension" name="Cluster," version="@galaxy_version@">
<tool id="scanpy_cluster_reduce_dimension" name="Cluster," version="@galaxy_version@" profile="@profile@">
<description>infer trajectories and embed with scanpy</description>
<macros>
<import>macros.xml</import>
Expand Down Expand Up @@ -58,7 +58,9 @@ This data is accessible using the inspect tool for AnnData
use_highly_variable=$method.use_highly_variable
]]></token>
</macros>
<expand macro="requirements"/>
<expand macro="requirements">
<requirement type="package" version="0.6.1">louvain</requirement>
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</expand>
<expand macro="version_command"/>
<command detect_errors="exit_code"><![CDATA[
@CMD@
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2 changes: 1 addition & 1 deletion tools/scanpy/filter.xml
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@@ -1,4 +1,4 @@
<tool id="scanpy_filter" name="Filter" version="@galaxy_version@">
<tool id="scanpy_filter" name="Filter" version="@galaxy_version@" profile="@profile@">
<description>with scanpy</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/scanpy/inspect.xml
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@@ -1,4 +1,4 @@
<tool id="scanpy_inspect" name="Inspect and manipulate" version="@galaxy_version@">
<tool id="scanpy_inspect" name="Inspect and manipulate" version="@galaxy_version@" profile="@profile@">
<description> with scanpy</description>
<macros>
<import>macros.xml</import>
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3 changes: 2 additions & 1 deletion tools/scanpy/macros.xml
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@@ -1,5 +1,6 @@
<macros>
<token name="@version@">1.4.4</token>
<token name="@version@">1.4.4.post1</token>
<token name="@profile@">19.01</token>
<token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>
<xml name="requirements">
<requirements>
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2 changes: 1 addition & 1 deletion tools/scanpy/normalize.xml
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@@ -1,4 +1,4 @@
<tool id="scanpy_normalize" name="Normalize" version="@galaxy_version@">
<tool id="scanpy_normalize" name="Normalize" version="@galaxy_version@" profile="@profile@">
<description>with scanpy</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/scanpy/plot.xml
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@@ -1,4 +1,4 @@
<tool id="scanpy_plot" name="Plot" version="@galaxy_version@">
<tool id="scanpy_plot" name="Plot" version="@galaxy_version@" profile="@profile@">
<description> with scanpy</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/scanpy/remove_confounders.xml
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@@ -1,4 +1,4 @@
<tool id="scanpy_remove_confounders" name="Remove confounders" version="@version@">
<tool id="scanpy_remove_confounders" name="Remove confounders" version="@version@" profile="@profile@">
<description>with scanpy</description>
<macros>
<import>macros.xml</import>
Expand Down