--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Dec 04 17:17:41 2018 -0500
@@ -0,0 +1,192 @@
+<macros>
+    <token name="@VERSION@">0.99.2</token>
+    <xml name="requirements">
+        <requirements>
+        <requirement type="package" version="@VERSION@">metaquantome</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="FUNC_FILE">
+        <param argument="--func_file" type="data" format="tabular" label="Functional file"
+            help="Tabular file with a peptide sequence column and a functional assignment column for GO-term, EC number, or COG."/>
+        <param argument="--pep_colname_func" type="text" label="Peptide column name" 
+            help="The column name within the function file that corresponds to the peptide sequences">
+            <validator type="empty_field"/>
+        </param>
+        <param argument="--func_colname" type="text" label="Functional column name" 
+            help="The column name within the function file with the functional terms">
+            <validator type="empty_field"/>
+        </param>
+    </xml>
+    <xml name="TAX_FILE">
+        <param argument="--tax_file" type="data" format="tabular" label="Taxonomy assignments file"/>
+        <param argument="--pep_colname_tax" type="text" label="Peptide column name" 
+            help="The column name within the taxonomy file that corresponds to the peptide sequences">
+            <validator type="empty_field"/>
+        </param>
+        <param argument="--tax_colname" type="text" label="Taxonomy column name"> 
+            <help>
+                Name of taxonomy column in taxonomy assignments file. The column must
+                be either NCBI taxids (strongly preferred) or taxonomy
+                names. Unipept name output is known to function well,
+                but other formats may not work.
+            </help>
+            <validator type="empty_field"/>
+        </param>
+    </xml>
+    <token name="@MAKE_SAMPS_TSV@"><![CDATA[
+        ### make samps config file 
+        #if $samps_args.samps_src == 'history':
+            cat '$samps_args.samps_file' > samp_file.tab &&
+        #else:
+            #set $samp_header = 'group\tcolnames'
+            echo -e '${samp_header}' > samp_file.tab &&
+            #for $s in $samps_args.samps
+                #set $sample = str($s.group_name) + '\t' + str($s.col_names)
+                echo -e '${sample}' >> samp_file.tab &&
+            #end for
+        #end if
+    ]]>
+    </token>
+    <token name="@DB_DIR@"><![CDATA[
+        #if $db_dir.db_loc == 'auto':
+            #if $mode_args.mode == 'taxfn'
+                --ft_func_data_dir data
+                --ft_tax_data_dir  data
+            #else
+                --data_dir data
+            #end if
+        ## #elif $db_dir.db_loc == 'cached':
+        #end if
+    ]]>
+    </token>
+    <xml name="data_dir">
+        <conditional name="db_dir">
+            <param argument="db_loc" type="select" label="Taxonomy and Functional Databases">
+                <option value="auto">automatcally load databases</option>
+                <!-- bioconda recipe would need to install the databases
+                <option value="pkg">use default metaquantome databases (not current)</option>
+                -->
+                <!-- requires a data_manager
+                <option value="cached">Use cached databases</option>
+                -->
+            </param>
+            <when value="auto"/>
+            <!-- bioconda recipe would need to install the databases
+            <when value="pkg"/>
+            -->
+            <!-- requires a data_manager
+            <when value="cached">
+            </when>
+            -->
+        </conditional>
+    </xml>
+    <token name="@COMMON_PARAMS@"><![CDATA[
+            --samps samp_file.tab
+            --mode '$mode_args.mode'
+            #if $mode_args.mode == 'f'
+                --func_file='$mode_args.func_file'
+                --func_colname='$mode_args.func_colname'
+                --pep_colname_func='$mode_args.pep_colname_func'
+                --ontology='$mode_args.ontology_args.ontology'
+                #if $mode_args.ontology_args.ontology == 'go'
+                    #if $mode_args.ontology_args.slim_down
+                        --slim_down
+                    #end if
+                #end if
+            #end if
+            #if $mode_args.mode =='t'
+                --tax_file='$mode_args.tax_file'
+                --tax_colname='$mode_args.tax_colname'
+                --pep_colname_tax='$mode_args.pep_colname_tax'
+            #end if
+            #if $mode_args.mode == 'ft'
+                --func_file='$mode_args.func_file'
+                --func_colname='$mode_args.func_colname'
+                --pep_colname_func='$mode_args.pep_colname_func'
+                --ontology=$mode_args.ontology
+                --tax_file='$mode_args.tax_file'
+                --tax_colname='$mode_args.tax_colname'
+                --pep_colname_tax='$mode_args.pep_colname_tax'
+                --ft_tar_rank='$mode_args.ft_tar_rank'
+            #end if
+    ]]>
+    </token>
+    <xml name="SAMPS">
+        <conditional name="samps_args">
+            <param argument="samps_src" type="select" label="Samples">
+                <option value="history">Use a samples dataset from your history</option>
+                <option value="build">Specify samples</option>
+            </param>
+            <when value="history">
+                <param name="samps_file" type="data" format="tabular" label="Samples file">
+                </param>
+            </when>
+            <when value="build">
+                <repeat name="samps" title="Samples">
+                    <param name="group_name" type="text" label="Group name"/>
+                    <param name="col_names" type="text" label="Column names of samples in group"/>
+                </repeat>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="common_params">
+        <conditional name="mode_args">
+            <param argument="--mode" type="select" label="Mode">
+                <option value="f">Functional analysis</option>
+                <option value="t">Taxonomic analysis</option>
+                <option value="ft">Functional-taxonomic interaction analysis</option>
+            </param>
+            <when value="f">
+                <expand macro="FUNC_FILE"/>
+                <conditional name="ontology_args">
+                    <param name="ontology" type="select" label="Ontology">
+                        <option value="go">GO Gene Ontology (column named 'go')</option>
+                        <option value="ec">EC Enzyme Commission (column named 'ec')</option>
+                        <option value="cog">COG (column named 'cog')</option>
+                    </param>
+                    <when value="go">
+                        <param argument="--slim_down" type="boolean" label="Use slim GO"/>
+                    </when>
+                    <when value="ec">
+                        <!-- do nothing -->
+                    </when>
+                    <when value="cog">
+                        <!-- do nothing -->
+                    </when>
+                </conditional>
+            </when>
+            <when value="t">
+                <expand macro="TAX_FILE"/>
+            </when>
+            <when value="ft">
+                <expand macro="FUNC_FILE"/>
+                <expand macro="TAX_FILE"/>
+                <param argument="--ft_tar_rank" type="select" label="rank at which to group taxonomy">
+                    <option value="species">species</option>
+                    <option value="genus" selected="true">genus</option>
+                    <option value="family">family</option>
+                    <option value="order">order</option>
+                    <option value="class">class</option>
+                    <option value="phylum">phylum</option>
+                    <option value="kingdom">kingdom</option>
+                </param>
+            </when>
+        </conditional>
+        <expand macro="SAMPS"/>
+    </xml>
+    <xml name="output_samples_choice">
+        <param name="output_samps" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output the samples fiile"/>
+    </xml>
+    <xml name="output_samples">
+        <data format="tabular" name="samples_file" label="${tool.name} on ${on_string} samples" from_work_dir="samp_file.tab">
+            <filter>output_samps == True</filter>
+        </data>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <yield />
+        </citations>
+    </xml>
+</macros>