comparison influx_si.xml @ 1:4e3d4318113b draft

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

0:9b03a930b08b

<tool id="influx_si" name="influx_si" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
   <description>metabolic flux analysis</description>
   <macros>
        <token name="@TOOL_VERSION@">5.1.0</token>
   </macros>
   <requirements>

       mkdir outdir && cd outdir &&

       #for $inp in $inp_all:
         #for $i in $inp:
           ln -s '$i' '$i.name' &&
         #end for
       #end for
       
       influx_$si.s_i
            $opt.noopt
            $opt.noscale
            #if $opt.meth != 'None':
               $opt.meth

            #end if

         #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 $input_main])}'
         > 'influx_${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 &&
       
       for f in *.pdf; do [ -e "\$f" ] && mv -f "\$f" "\$f".pdf || true; done &&

              <option value="i">instationary</option>
          </param>
          <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.">
                  <option value="None">None</option>
                  <option value="1">1</option>
                  <option value="2">2</option>
                  <option value="1,2">1,2</option>
              </param>

        <param argument="--TIMEIT" type="boolean" checked="false" truevalue="--TIMEIT" falsevalue="" label="measure timings" optional="true" help="developer option: measure cpu time or not" />
        <param argument="--tblimit" type="integer" min="0" value="0" label="Python traceback limit" optional="true" help="developer option: set trace back limit for Python error messages" />
      </section>
   </inputs>
   <outputs>
      <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>
   </outputs>
   <tests>
      <test>
         <param name="input_main" value="e_coli.ftbl" />
         <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>
      </test>
      <test>
         <param name="input_main" value="e_coli.ftbl,e_coli_growth.ftbl" />
         <conditional name="si">
            <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" />
         </output_collection>
      </test>
      <test>
         <param name="input_main" value="e_coli_i.ftbl" />
         <conditional name="si">
            <param name="s_i" value="i" />
            <param name="input_ti" value="e_coli_msen.txt" />
            <!--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" />
         </output_collection>
      </test>
      <test>
         <param name="input_main" value="e_coli_1-Glc_exact.ftbl" />
         <param name="input_aux" value="e_coli_U-Glc_exact.ftbl" />
         <conditional name="si">
            <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" />
         </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>
      <citation type="bibtex">
         @misc{githubinflux,

1:4e3d4318113b

<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>
   </macros>
   <requirements>

       mkdir outdir && cd outdir &&

       #for $inp in $inp_all:
         #for $i in $inp:
           ln -s '$i' '$i.element_identifier' &&
         #end for
       #end for

       influx_$si.s_i
            $opt.noopt
            $opt.noscale
            #if $opt.meth != 'None':
               $opt.meth

            #end if

         #if $si.s_i == 'i' and $si.time_order:
           --time_order='$si.time_order'
         #end if
         '${"' '".join([str($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 &&
       
       for f in *.pdf; do [ -e "\$f" ] && mv -f "\$f" "\$f".pdf || true; done &&

              <option value="i">instationary</option>
          </param>
          <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" 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>
                  <option value="1,2">1,2</option>
              </param>

        <param argument="--TIMEIT" type="boolean" checked="false" truevalue="--TIMEIT" falsevalue="" label="measure timings" optional="true" help="developer option: measure cpu time or not" />
        <param argument="--tblimit" type="integer" min="0" value="0" label="Python traceback limit" optional="true" help="developer option: set trace back limit for Python error messages" />
      </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>
   </outputs>
   <tests>
      <test>
         <param name="input_main" value="e_coli.ftbl" />
         <conditional name="si">
            <param name="s_i" value="s" />
         </conditional>
         <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>
         <param name="input_main" value="e_coli.ftbl,e_coli_growth.ftbl" />
         <conditional name="si">
            <param name="s_i" value="s" />
         </conditional>
         <output_collection name="influx_si_output" type="list">
            <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>
         <param name="input_main" value="e_coli_i.ftbl" />
         <conditional name="si">
            <param name="s_i" value="i" />
            <param name="input_ti" value="e_coli_msen.txt" />
            <!--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">
               <assert_contents>
                  <has_n_lines n="47"/>
                  <has_line_matching expression="^end.*"/>
               </assert_contents>
            </element>
         </output_collection>
      </test>
      <test>
         <param name="input_main" value="e_coli_1-Glc_exact.ftbl" />
         <param name="input_aux" value="e_coli_U-Glc_exact.ftbl" />
         <conditional name="si">
            <param name="s_i" value="s" />
         </conditional>
         <output_collection name="influx_si_output" type="list">
            <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[
   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>
      <citation type="bibtex">
         @misc{githubinflux,