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Matchms networking: error message #443

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Matchms networking: error message #443

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4eef6cd
matchms networking: skip configfile
bernt-matthias Nov 23, 2023
e18ba72
add test with wrong id key
bernt-matthias Nov 23, 2023
07571f5
bump
bernt-matthias Nov 23, 2023
68c15f4
Merge branch 'master' into topic/matchms-nw-fix
hechth Jul 25, 2024
fc80358
Merge branch 'master' into topic/matchms-nw-fix
hechth Aug 15, 2024
645e612
Merge branch 'master' into topic/matchms-nw-fix
hechth May 16, 2025
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47 changes: 27 additions & 20 deletions tools/matchms/matchms_networking.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="matchms_networking" name="matchms networking" version="@TOOL_VERSION@+galaxy0" profile="21.09">
<tool id="matchms_networking" name="matchms networking" version="@TOOL_VERSION@+galaxy1" profile="21.09">
<description>create similarity network graph from matchms similarity scores</description>

<macros>
Expand All @@ -17,32 +17,26 @@
</requirements>

<command detect_errors="aggressive"><![CDATA[
sh ${matchms_networking_cli}
python3 '${__tool_directory__}/matchms_networking_wrapper.py'
--score_name '${score_layer_name}'
--graph_format '$graph_format'
--identifier '$identifier_key'
--top_n '$top_n'
--max_links '$max_links'
--score_cutoff '$score_cutoff'
--link_method '$link_method'
#if $keep_unconnected_nodes
--keep_unconnected_nodes
#end if
'$scores'
'$similarity_network_file'
]]></command>

<environment_variables>
<environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
<environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
</environment_variables>

<configfiles>
<configfile name="matchms_networking_cli">
python3 ${__tool_directory__}/matchms_networking_wrapper.py \
--score_name '${score_layer_name}' \
--graph_format '$graph_format' \
--identifier '$identifier_key' \
--top_n '$top_n' \
--max_links '$max_links' \
--score_cutoff '$score_cutoff' \
--link_method '$link_method' \
#if $keep_unconnected_nodes
--keep_unconnected_nodes \
#end if
'$scores' \
'$similarity_network_file'
</configfile>
</configfiles>

<inputs>
<param label="Similarity scores" name="scores" type="data" format="json"
help="matchms similarity-scores file."/>
Expand Down Expand Up @@ -90,6 +84,19 @@
</outputs>

<tests>

<test expect_exit_code="1" expect_failure="true">
<param name="scores" value="scores.json" ftype="json"/>
<param name="graph_format" value="cyjs"/>
<param name="max_links" value="5"/>
<param name="score_cutoff" value="0.3"/>
<param name="identifier_key" value="COMPOUND_NAME"/>
<param name="keep_unconnected_nodes" value="false"/>
<assert_stderr>
<has_text text="ValueError: None cannot be a node"/>
</assert_stderr>
</test>

<test>
<param name="scores" value="scores.json" ftype="json"/>
<param name="graph_format" value="graphml"/>
Expand Down
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