diff reduce-model.xml @ 0:233d87b56795 draft default tip

"planemo upload for repository https://github.com/brsynth/straindesign commit ef548ee3fe2740006c95cafb67504c72ef509575"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reduce-model.xml	Thu Sep 29 18:48:17 2022 +0000
@@ -0,0 +1,98 @@
+<tool id="reduce-model" name="reduce-model" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
+    <description>Delete genes and associated reactions in a model.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command detect_errors="exit_code"><![CDATA[
+        python -m straindesign reduce-model
+            @CMD_INPUT_MODEL@
+            #if $sd_strategy.sd_cond:
+                --input-straindesign-file '$sd_strategy.sd_tsv'
+                --parameter-strategy-str '$sd_strategy.sd_strategy_str'
+            #end if
+            --output-file-sbml '$output_sbml'
+            #if str($input_gene_str) != ''
+                #set $sgs = str($input_gene_str)
+                --input-gene-str #echo $sgs
+            #end if
+    ]]></command>
+    <expand macro="env_variables"/>
+    <inputs>
+        <expand macro="input_model_sbml"/>
+        <conditional name="sd_strategy">
+            <param name="sd_cond" type="boolean" checked="false" label="Fill with the output of StrainDesign simulate-deletion"/>
+            <when value="true">
+                <param name="sd_tsv" type="data" format="tsv" label="StrainDesign simulate-deletion output"/>
+                <param name="sd_strategy_str" type="select" label="Strategy">
+                    <option value="yield-max" selected="True">Yield Max</option>
+                    <option value="gene-max">Gene Max</option>
+                    <option value="gene-min"> Gene Min</option>
+                </param>
+            </when>
+            <when value="false"/>
+        </conditional>
+        <param name="input_gene_str" type="text" value="" label="Gene IDs. Multiple genes are separated by space">
+            <validator type="regex" message="No special characters allowed">^(?:[ \w.-])*$</validator>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_sbml" format="sbml" label="${tool.name}" />
+    </outputs>
+    <tests>
+        <test>
+            <!--  test 1  -->
+            <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
+            <param name="input_gene_str" value="b4208 b4208 b3919"/>
+            <output name="output_sbml" ftype="sbml">
+                <assert_contents>
+                    <is_valid_xml/>
+                    <not_has_text text="b4208"/>
+                    <not_has_text text="b3919"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <!--  test 2  -->
+            <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
+            <param name="sd_cond" value="true"/>
+            <param name="sd_tsv" ftype="tabular" value="simulate_deletion.butanol.iAF1260.tsv"/>
+            <output name="output_sbml" ftype="sbml">
+                <assert_contents>
+                    <is_valid_xml/>
+                    <not_has_text text="b3919"/>
+                    <not_has_text text="b0529"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <!--  test 3  -->
+            <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
+            <param name="sd_cond" value="true"/>
+            <param name="sd_tsv" ftype="tabular" value="simulate_deletion.butanol.iAF1260.tsv"/>
+            <param name="input_gene_str" value="b4208 b4208 b3919"/>
+            <output name="output_sbml" ftype="sbml">
+                <assert_contents>
+                    <is_valid_xml/>
+                    <not_has_text text="b4208"/>
+                    <not_has_text text="b3919"/>
+                    <not_has_text text="b0529"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_TITLE@
+
+This tool helps to delete some genes provided either from **simulate-deletion¨** or provided by their ids, in an SBML model.
+If you provide a TSV file coming from the **simulate-deletion** commands either the file is cleanned by hand and contains one line or the program tries to identify which genes will be deleted by applying the suited strategy:
+* yield-max: the combination of genes with the maximum amount of yiel is taken
+* gene-max: the combination of genes with the maximum number of genes is taken
+* gene-min: the combination of genes with the minimum number of genes is taken
+
+@HELP_LINK@
+    ]]></help>
+    <expand macro="creator"/>
+    <expand macro="citation"/>
+</tool>