comparison metaquantome_viz.xml @ 3:5bbedd902998 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2"

2:51bc1ccad6aa

            #end if
        #elif $mode_args.plot.plottype == 'heatmap':
            #if $mode_args.plot.heatmap.filter_to_sig:
              --filter_to_sig
              --alpha=$mode_args.plot.heatmap.alpha
              --fc_corr_p='mode_args.plot.fc_corr_p'
            #end if
            #if $mode_args.plot.feature_cluster_size:
                --feature_cluster_size='$mode_args.plot.feature_cluster_size'
            #end if
            #if $mode_args.plot.sample_cluster_size:

            <p>
              If text is cut off or the plot is not displaying properly,
              the easiest fix is to increase the plot dimensions
            </p>
          </body>
        </html>" > wrapped_outfile.html
    && >&2 ls
    #if $mode_args.plot.plottype in ["heatmap"]
        && mv 'feature_cluster_${safename}.txt' '$heatmap_feature_cluster'
        && mv 'sample_cluster_${safename}.txt' '$heatmap_sample_cluster'
    #end if
    #if $mode_args.plot.plottype in ["pca"]
        && mv 'PC_data_${safename}.txt' '$pca_sample_cluster'
    #end if
      
    ]]></command>
    <inputs>
      <param argument="--infile" type="data"
        format="tabular" label="Tabular file from metaQuantome stats or metaQuantome filter" help=""/>
      <expand macro="SAMPS"/>

        from_work_dir="plotdata.tab">
        <filter>mode_args['plot']['plottype'] in ["bar", "volcano"]</filter>
      </data>
      
      <data format="tabular" name="heatmap_feature_cluster"
        label="${tool.name} on ${on_string}: ${mode_args.plot.plottype} feature cluster data">
        <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
      </data>
      <data format="tabular" name="heatmap_sample_cluster"
        label="${tool.name} on ${on_string}: ${mode_args.plot.plottype} sample cluster data">
        <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
      </data>
      
      <data format="tabular" name="pca_sample_cluster"
        label="${tool.name} on ${on_string}: ${mode_args.plot.plottype} sample cluster data">
        <filter>mode_args['plot']['plottype'] in ["pca"]</filter>
      </data>
      
    </outputs>
    <tests>

                    <has_text text="To download the image" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
             <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
             <param name="mode" value="t" />
             <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
             <param name="plottype" value="heatmap" />
             <output name="wrapped_outfile">
                <assert_contents>
                    <has_text text="To download the image" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">
             <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
             <param name="mode" value="t" />

             <param name="plottype" value="pca" />
             <output name="wrapped_outfile">
                <assert_contents>
                    <has_text text="To download the image" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">
             <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
             <param name="mode" value="f" />
             <param name="ontology" value="go" />

3:5bbedd902998

            #end if
        #elif $mode_args.plot.plottype == 'heatmap':
            #if $mode_args.plot.heatmap.filter_to_sig:
              --filter_to_sig
              --alpha=$mode_args.plot.heatmap.alpha
              --fc_corr_p='$mode_args.plot.heatmap.fc_corr_p'
            #end if
            #if $mode_args.plot.feature_cluster_size:
                --feature_cluster_size='$mode_args.plot.feature_cluster_size'
            #end if
            #if $mode_args.plot.sample_cluster_size:

            <p>
              If text is cut off or the plot is not displaying properly,
              the easiest fix is to increase the plot dimensions
            </p>
          </body>
        </html>" > wrapped_outfile.html &&
        if test -f 'feature_cluster_${infile.name}.txt'; then mv 'feature_cluster_${infile.name}.txt' feature_cluster_data.txt; fi && 
        if test -f 'sample_cluster_${infile.name}.txt'; then mv 'sample_cluster_${infile.name}.txt' sample_cluster_data.txt; fi &&
        if test -f 'PC_Data_${infile.name}.txt'; then mv 'PC_Data_${infile.name}.txt' PC_Data.txt; fi

    ]]></command>
    <inputs>
      <param argument="--infile" type="data"
        format="tabular" label="Tabular file from metaQuantome stats or metaQuantome filter" help=""/>
      <expand macro="SAMPS"/>

        from_work_dir="plotdata.tab">
        <filter>mode_args['plot']['plottype'] in ["bar", "volcano"]</filter>
      </data>
      
      <data format="tabular" name="heatmap_feature_cluster"
        label="${mode_args.plot.plottype}: feature cluster data"
        from_work_dir="feature_cluster_data.txt">
        <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
      </data>
      <data format="tabular" name="heatmap_sample_cluster"
        label="${mode_args.plot.plottype}: sample cluster data"
        from_work_dir="sample_cluster_data.txt">
        <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
      </data>
      
      <data format="tabular" name="pca_sample_cluster"
        label="${mode_args.plot.plottype}: sample cluster data"
        from_work_dir="PC_Data.txt">
        <filter>mode_args['plot']['plottype'] in ["pca"]</filter>
      </data>
      
    </outputs>
    <tests>

                    <has_text text="To download the image" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
            <param name="mode" value="t" />
            <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
            <param name="plottype" value="heatmap" />
            <param name="filter_to_sig" />
            <param name="alpha" value="0.05" />
            <param name="fc_corr_p" value="corrected_p_NS_over_WS" />
            <param name="feature_cluster_size" value="2" />
            <param name="sample_cluster_size" value="2" />
            <output name="wrapped_outfile">
              <assert_contents>
                  <has_text text="To download the image" />
              </assert_contents>
            </output>
            <output name="heatmap_feature_cluster">
              <assert_contents>
                  <has_text text="481" />
              </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">
             <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
             <param name="mode" value="t" />

             <param name="plottype" value="pca" />
             <output name="wrapped_outfile">
                <assert_contents>
                    <has_text text="To download the image" />
                </assert_contents>
              </output>
        </test>
        <test expect_num_outputs="2">
             <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
             <param name="mode" value="f" />
             <param name="ontology" value="go" />