diff influx_si.xml @ 1:4e3d4318113b draft

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit e9183269ad5b2e8f4551f301dc736df330aa73c6

--- a/influx_si.xml	Mon May 04 03:24:12 2020 -0400
+++ b/influx_si.xml	Wed Sep 13 19:52:44 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="influx_si" name="influx_si" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
+<tool id="influx_si" name="influx_si" version="@TOOL_VERSION@+galaxy1">
    <description>metabolic flux analysis</description>
    <macros>
         <token name="@TOOL_VERSION@">5.1.0</token>
@@ -17,10 +17,10 @@
 
        #for $inp in $inp_all:
          #for $i in $inp:
-           ln -s '$i' '$i.name' &&
+           ln -s '$i' '$i.element_identifier' &&
          #end for
        #end for
-       
+
        influx_$si.s_i
             $opt.noopt
             $opt.noscale
@@ -81,7 +81,7 @@
          #if $si.s_i == 'i' and $si.time_order:
            --time_order='$si.time_order'
          #end if
-         '${"' '".join([str($in_m.name) for $in_m in $input_main])}'
+         '${"' '".join([str($in_m.element_identifier) for $in_m in $input_main])}'
          > 'influx_${si.s_i}.stdout.txt' 2>'influx_${si.s_i}.stderr.txt'; res="\$?" &&
        
        for f in *.ftbl *.log *.err *.R *.kvh *.attrs; do mv -f "\$f" "\$f".txt || true; done &&
@@ -101,7 +101,7 @@
           <when value="s"/>
           <when value="i">
               <param type="data" name="input_ti" label="time course data" format="txt,tsv" multiple="true"/>
-              <param argument="--time_order" type="select" label="time order for ODE solving" display="radio" optional="true" help="Order 2 is more precise but more time consuming. The value &#x27;1,2&#x27; makes to start solving the ODE with the first order scheme then continues with the order 2.">
+              <param argument="--time_order" type="select" label="time order for ODE solving" optional="true" help="Order 2 is more precise but more time consuming. The value &#x27;1,2&#x27; makes to start solving the ODE with the first order scheme then continues with the order 2.">
                   <option value="None">None</option>
                   <option value="1">1</option>
                   <option value="2">2</option>
@@ -147,6 +147,7 @@
       </section>
    </inputs>
    <outputs>
+      <!-- TODO: this should probably not be a collection, also name_and_ext probably does not work correctly for all elements-->
       <collection name="influx_si_output" type="list" label="influx_${si.s_i}_on_${on_string}">
          <discover_datasets pattern="__name_and_ext__" directory="outdir" visible="false"/>
       </collection>
@@ -157,8 +158,13 @@
          <conditional name="si">
             <param name="s_i" value="s" />
          </conditional>
-         <output_collection name="influx_si_output" type="list">
-            <element name="e_coli.log" ftype="txt" file="e_coli.log" compare="sim_size" delta="100" />
+         <output_collection name="influx_si_output" type="list" count="11">
+            <element name="e_coli.log" ftype="txt">
+               <assert_contents>
+                  <has_n_lines n="38"/>
+                  <has_line_matching expression="^end.*"/>
+               </assert_contents>
+            </element>
          </output_collection>
       </test>
       <test>
@@ -167,7 +173,12 @@
             <param name="s_i" value="s" />
          </conditional>
          <output_collection name="influx_si_output" type="list">
-            <element name="e_coli_growth.log" ftype="txt" file="e_coli_growth.log" compare="sim_size" delta="100" />
+            <element name="e_coli_growth.log" ftype="txt">
+               <assert_contents>
+                  <has_n_lines n="45"/>
+                  <has_line_matching expression="^end.*"/>
+               </assert_contents>
+            </element>
          </output_collection>
       </test>
       <test>
@@ -178,7 +189,12 @@
             <!--param name="time_order" value="1,2" /--> <!--How to pass single value with comma in it?-->
          </conditional>
          <output_collection name="influx_si_output" type="list">
-            <element name="e_coli_i.log" ftype="txt" file="e_coli_i.log" compare="sim_size" delta="100" />
+            <element name="e_coli_i.log" ftype="txt">
+               <assert_contents>
+                  <has_n_lines n="47"/>
+                  <has_line_matching expression="^end.*"/>
+               </assert_contents>
+            </element>
          </output_collection>
       </test>
       <test>
@@ -188,13 +204,16 @@
             <param name="s_i" value="s" />
          </conditional>
          <output_collection name="influx_si_output" type="list">
-            <element name="e_coli_1-Glc_exact.log" file="e_coli_1-Glc_exact.log" compare="sim_size" delta="100" />
+            <element name="e_coli_1-Glc_exact.log" ftype="txt">
+               <assert_contents>
+                  <has_n_lines n="40"/>
+                  <has_line_matching expression="^end.*"/>
+               </assert_contents>
+            </element>
          </output_collection>
       </test>
    </tests>
    <help><![CDATA[
-   Usage: influx_s [options] /path/to/FTBL_file1 [FTBL_file2 [...]]
-
    Optimize free fluxes and optionaly metabolite concentrations of a given static metabolic network defined in an FTBL file to fit 13C data provided in the same FTBL file.
    ]]></help>
    <citations>