# HG changeset patch
# User tduigou
# Date 1682904852 0
# Node ID 164ccfcd18ecbe8c25cf224ae51acfb2cf6e5236
# Parent  34a9d136a5bf42ed188c26f251e7f43d046ddd36
planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6

diff -r 34a9d136a5bf -r 164ccfcd18ec config/job_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/config/job_conf.xml	Mon May 01 01:34:12 2023 +0000
@@ -0,0 +1,1 @@
+    <tool id="selenzy_wrapper" destination="local" />
diff -r 34a9d136a5bf -r 164ccfcd18ec config/tool_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/config/tool_conf.xml	Mon May 01 01:34:12 2023 +0000
@@ -0,0 +1,3 @@
+  <section id="sbc-util" name="SynBioCAD Utilities">
+    <tool file="synbiocad-galaxy-wrappers/selenzy_wrapper/selenzy_wrapper.xml" />
+  </section>
\ No newline at end of file
diff -r 34a9d136a5bf -r 164ccfcd18ec selenzy.xml
--- a/selenzy.xml	Tue Feb 08 11:12:28 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,96 +0,0 @@
-<tool id="selenzy-wrapper" name="Selenzyme" version="@TOOL_VERSION@" profile="19.09">
-    <description>Performs enzyme selection from a reaction query</description>
-    <macros>
-        <token name="@TOOL_VERSION@">0.2.0</token>
-    </macros>
-    <requirements>
-        <requirement type="package" version="@TOOL_VERSION@">selenzy_wrapper</requirement>
-    </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-        python -m selenzy_wrapper '$pathway' '$uniprot_ids'
-        --nb_targets '$adv.nb_targets'
-        --d '$adv.direction'
-        #if str($adv.NoMSA) == "false":
-            --NoMSA
-        #end if
-        --host_taxID '$adv.host_taxID'
-        #if str($adv.enzyme_taxIDs) != "":
-            --enzyme_taxIDs '$adv.enzyme_taxIDs'
-        #end if
-        --nb_ids '$adv.nb_ids'
-        --to_csv '$uniprot_ids_csv'
-    ]]></command>
-    <inputs>
-        <param name="pathway" type="data" format="xml" label="Pathway (SBML)" />
-        <section name="adv" title="Advanced Options" expanded="false">
-            <param name="host_taxID" type="integer" value="83333" label="Host taxon ID" />
-            <param name="enzyme_taxIDs" type="text" value="" label="Comma separated taxon IDs of output enzyme sequences" />
-            <param name="nb_ids" type="integer" value="-1" label="Number of uniprot IDs with top score to keep" />
-            <param name="nb_targets" type="integer" value="500" label="Number of targets to display in results" />
-            <param name="direction" type="float" value="0" label="Use similiarity values for preferred reaction direction only" />
-            <param name="NoMSA" type="boolean" checked="true" display="checkboxes" label="Do not compute MSA/conservation scores ?" />
-        </section>
-    </inputs>
-    <outputs>
-        <data name="uniprot_ids" format="xml" label="Uniprot IDs" />
-        <data name="uniprot_ids_csv" format="csv" label="Uniprot IDs" />
-    </outputs>
-    <tests>
-        <test>
-        <!-- test 1: check if identical outputs are produced with default parameters  -->
-            <param name="pathway" value="pathway.xml" />
-            <output name="uniprot_ids" file="uniprod_ids_out.xml" ftype="xml" compare="diff" sort="true"/>
-            <output name="uniprot_ids_csv" file="uniprod_ids_out.csv" ftype="csv" compare="diff"/>
-        </test>
-    </tests>
-    <help><![CDATA[
-Selenzyme
-================
-
-Performs enzyme selection from a reaction query.
-
-Input
------
-
-* **pathway_file**\ : (string) path to pathway file
-* **nb_targets**\ : (integer) Number of targets to display in results (before taxon IDs filtering) [default = 20]
-* **nb_ids**\ : (integer) Number of enzyme IDs to display in results (after taxon IDs filtering) [default = -1 (no limit)]
-* **direction**\ : (float) Use similiarity values for preferred reaction direction only [default=0 (OFF)]
-* **NoMSA**\ : (boolean) Do not compute MSA/conservation scores
-* **host_taxID**\ : (string) Taxon ID of the chassis (default: 83333 [E. coli K12])
-* **enzyme_taxIDs**\ : (string) Comma separated taxon IDs of output enzyme sequences
-
-Output
-------
-
-* **outfile**\ : (string) Path to output file
-
-Project Links
-------------------
-
-* `GitHub <https://github.com/brsynth/selenzy-wrapper>`_
-
-Version
-----------
-
-0.2.0
-
-Authors
--------
-* **Joan Hérisson**
-
-License
--------
-
-* `MIT <https://github.com/brsynth/selenzy-wrapper/blob/master/LICENSE>`_
-
-Acknowledgments
----------------
-
-* Thomas Duigou
-
-    ]]></help>
-    <citations>
-        <citation type="doi">10.1093/bioinformatics/bty065</citation>
-    </citations>
-</tool>
\ No newline at end of file
diff -r 34a9d136a5bf -r 164ccfcd18ec selenzy_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/selenzy_wrapper.xml	Mon May 01 01:34:12 2023 +0000
@@ -0,0 +1,97 @@
+<tool id="selenzy-wrapper" name="Selenzyme" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
+    <description>Performs enzyme selection from a reaction query</description>
+    <macros>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@TOOL_VERSION@">0.3.0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">selenzy_wrapper</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python -m selenzy_wrapper '$pathway' '$uniprot_ids'
+        --nb_targets '$adv.nb_targets'
+        --d '$adv.direction'
+        $adv.NoMSA
+        --host_taxID '$adv.host_taxID'
+        #if str($adv.enzyme_taxIDs) != "":
+            --enzyme_taxIDs '$adv.enzyme_taxIDs'
+        #end if
+        --nb_ids '$adv.nb_ids'
+        --to_csv '$uniprot_ids_csv'
+        --data-path "\${TMPDIR:-.}"
+    ]]></command>
+    <inputs>
+        <param name="pathway" type="data" format="sbml" label="Pathway (SBML)" />
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param name="host_taxID" type="integer" value="83333" label="Host taxon ID" help="Taxon ID of the chassis (default: 83333 [E. coli K12])" />
+            <param name="enzyme_taxIDs" type="text" value="" label="Comma separated taxon IDs of output enzyme sequences" />
+            <param name="nb_ids" type="integer" value="-1" label="Number of uniprot IDs with top score to keep" help=" Number of enzyme IDs to display in results (after taxon IDs filtering) [default = -1 (no limit)]" />
+            <param name="nb_targets" type="integer" value="500" min="1" label="Number of targets to display in results" help="Number of targets to display in results (before taxon IDs filtering) [default = 500]" />
+            <param name="direction" type="float" value="0" label="Use similarity values for preferred reaction direction only" help="You can choose to rank similarities in both reaction directions or to use only the direction of the reaction based on a consensus list that has been generated according to reaction information based on curated information from MetaCyc (Metabolic Pathway Database) [default=0 (OFF)]" />
+            <param argument="--NoMSA" type="boolean" falsevalue="--NoMSA" truevalue="" checked="true" display="checkboxes" label="Do not compute MSA/conservation scores ?" help="Do not compute Multiple Sequence Alignment and conservation scores ? (MSA scores are computed by default)" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="uniprot_ids" format="sbml" label="Uniprot IDs (SBML)" />
+        <data name="uniprot_ids_csv" format="csv" label="Uniprot IDs (CSV)" />
+    </outputs>
+    <tests>
+        <test>
+        <!-- test 1: check if identical outputs are produced with default parameters  -->
+            <param name="pathway" value="pathway.xml" />
+            <output name="uniprot_ids" file="uniprod_ids_out.xml" compare="diff" sort="true"/>
+            <output name="uniprot_ids_csv" file="uniprod_ids_out.csv" ftype="csv" compare="diff"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Selenzyme
+================
+
+Selenzyme searches for enzymes corresponding to each reaction of the pathway. It performs a reaction similarity search in the reference reaction database `MetaNetX <https://www.metanetx.org/>`_ and outputs an updated SBML file annotated with the enzyme UniProt IDs, as well as in CSV format.
+
+Input
+-----
+
+* **Pathway (SBML)**\ : SBML pathway file
+* **Number of targets to display in results**\ : (integer) Number of targets to display in results (before taxon IDs filtering) [default = 500]
+* **Number of uniprot IDs with top score to keep**\ : (integer) Number of enzyme IDs to display in results (after taxon IDs filtering) [default = -1 (no limit)]
+* **Use similarity values for preferred reaction direction only**\ : (float) Use similarity values for preferred reaction direction only [default=0 (OFF)]
+* **Do not compute MSA/conservation scores ?**\ : (boolean) Do not compute Multiple Sequence Alignment and conservation scores ? (MSA scores are computed by default)
+* **Host taxon ID**\ : (string) Taxon ID of the chassis (default: 83333 [E. coli K12])
+* **Comma separated taxon IDs of output enzyme sequences**\ : (string) Comma separated taxon IDs of output enzyme sequences
+
+Output
+------
+
+* **Uniprot IDs (SBML)**\ : Annotated SBML pathway.
+* **Uniprot IDs (CSV)**\ : Annotated CSV pathway.
+
+Project Links
+------------------
+
+* `GitHub <https://github.com/brsynth/selenzy-wrapper>`_
+
+Version
+----------
+
+0.3.0
+
+Authors
+-------
+* **Joan Hérisson**
+
+License
+-------
+
+* `MIT <https://github.com/brsynth/selenzy-wrapper/blob/master/LICENSE>`_
+
+Acknowledgments
+---------------
+
+* Thomas Duigou
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/bty065</citation>
+    </citations>
+</tool>
\ No newline at end of file