# HG changeset patch
# User galaxyp
# Date 1543961861 18000
# Node ID b17b03126d40a41daf916c56b92721a831426e34

planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty

diff -r 000000000000 -r b17b03126d40 macros.xml
--- /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>
diff -r 000000000000 -r b17b03126d40 metaquantome_expand.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaquantome_expand.xml	Tue Dec 04 17:17:41 2018 -0500
@@ -0,0 +1,76 @@
+<tool id="metaquantome_expand" name="MetaQuantome Expand" version="@VERSION@.0">
+    <description>annotated functional or taxonomy terms to include all terms</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p data && #slurp
+        @MAKE_SAMPS_TSV@
+        metaquantome expand
+        @COMMON_PARAMS@
+        @DB_DIR@
+        #if $input.input_type == 'nopep':
+            --nopep --nopep_file='$input.nopep_file' 
+        #else:
+            --int_file='$input.int_file' 
+            --pep_colname_int='$input.pep_colname_int'
+        #end if
+       --outfile='$outfile'
+    ]]></command>
+    <inputs>
+        <expand macro="data_dir"/>
+        <expand macro="common_params"/>
+        <conditional name="input">
+            <param name="input_type" type="select" label="Select input data">
+                <option value="int">tabular intensity file with peptide column</option>
+                <option value="nopep">file without a peptide column</option>
+            </param>
+            <when value="int">
+                <param argument="--int_file" type="data" format="tabular" label="intensity data"
+                    help=""/>
+                <param argument="--pep_colname_int" type="text" value="" label="Peptide column name" 
+                    help="The column name within the intensity file that corresponds to the peptide sequences">
+                    <validator type="empty_field"/>
+                </param>
+            </when>
+            <when value="nopep">
+                <param argument="--nopep_file" type="data" format="tabular" label="intensity data"
+                    help=""/>
+            </when>
+        </conditional>
+        <expand macro="output_samples_choice"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="outfile" label="${tool.name} on ${on_string} expanded"/>
+        <expand macro="output_samples"/>
+    </outputs>
+    <tests>
+        <test>
+            <!-- expand('f', sinfo=TTEST_SINFO, int_file=int, pep_colname_int='peptide', pep_colname_func='peptide',
+                         pep_colname_tax='peptide', data_dir=GO_TEST_DIR, outfile=expanded, func_file=func,
+                         func_colname='go', ontology='go') -->
+             <param name="int_file" value="int_ttest.tab" ftype="tabular"/>
+             <param name="pep_colname_int" value="peptide" />
+             <param name="func_file" value="multiple_func.tab" />
+             <param name="pep_colname_func" value="peptide" />
+             <param name="func_colname" value="go"/>
+             <param name="mode" value="f" />
+             <param name="ontology" value="go" />
+             <param name="samps_src" value="build" />
+             <repeat name="samps">
+                 <param name="group_name" value="s1"/>
+                 <param name="col_names" value="int1,int2,int3"/>
+             </repeat>
+             <repeat name="samps">
+                 <param name="group_name" value="s2"/>
+                 <param name="col_names" value="int4,int5,int6"/>
+             </repeat>
+             <output name="outfile" file="go_expanded.tab" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        help
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff -r 000000000000 -r b17b03126d40 metaquantome_filter.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaquantome_filter.xml	Tue Dec 04 17:17:41 2018 -0500
@@ -0,0 +1,81 @@
+<tool id="metaquantome_filter" name="MetaQuantome Filter" version="@VERSION@.0">
+    <description>for quality, redundancy, and sample coverage</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        @MAKE_SAMPS_TSV@
+        metaquantome filter
+        @COMMON_PARAMS@
+        --expand_file '$expand_file'
+        --min_peptides $min_peptides 
+        #if $min_pep_nsamp:
+            --min_pep_nsamp max($min_peptides,$min_pep_nsamp)
+        #else
+            --min_pep_nsamp all
+        #end if
+        --min_children_non_leaf $min_children_non_leaf
+        #if $min_child_nsamp:
+            --min_child_nsamp max($min_peptides,$min_child_nsamp)
+        #else
+            --min_child_nsamp all
+        #end if
+        --qthreshold $qthreshold
+        --outfile='$output'
+    ]]></command>
+    <inputs>
+        <expand macro="common_params"/>
+        <param argument="--expand_file" type="data" format="tabular" label="metaquantome expand file"
+                    help=""/>
+        <param argument="--min_peptides" type="integer" value="0" min="0" label="min_peptides">
+            <help>
+                Used for filtering to well-supported annotations. The
+                number of peptides providing evidence for a term is
+                the number of peptides directly annotated with that
+                term plus the number of peptides annotated with any of
+                its descendants. Terms with a number of peptides
+                greater than or equal to min_peptides are retained.
+                The default is 0.
+            </help>
+        </param>
+        <param argument="--min_pep_nsamp" type="integer" value="" min="0" optional="true" label="min_pep_nsamp">
+            <help>
+                Number of samples per group that must meet or exceed
+                min_peptides. Default is 'all'.
+            </help>
+        </param>
+        <param argument="--min_children_non_leaf" type="integer" value="0" min="0" label="min_children_non_leaf">
+            <help>
+                Used for filtering to informative annotations. A term
+                is retained if it has a number of children greater
+                than or equal to min_children_non_leaf. The default is 0.
+            </help>
+        </param>
+        <param argument="--min_child_nsamp" type="integer" value="" min="0" optional="true" label="min_child_nsamp">
+            <help>
+                Number of samples per group that must meet or exceed
+                min_children_nsamp. Default is 'all'.
+            </help>
+        </param>
+        <param argument="--qthreshold" type="integer" value="3" min="0" label="qthreshold">
+            <help>
+                Minimum number of intensities in each sample group.
+                Any functional/taxonomic term with lower number of
+                per-group intensities will be filtered out. The
+                default is 3, because this is the minimum number for
+                t-tests.
+            </help>
+        </param>
+
+        <expand macro="output_samples_choice"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="outfile" label="${tool.name} on ${on_string} filtered"/>
+        <expand macro="output_samples"/>
+    </outputs>
+    <help><![CDATA[
+        TODO: Fill in help.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff -r 000000000000 -r b17b03126d40 metaquantome_stat.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaquantome_stat.xml	Tue Dec 04 17:17:41 2018 -0500
@@ -0,0 +1,67 @@
+<tool id="metaquantome_stat" name="MetaQuantome Stats" version="@VERSION@.0">
+    <description>differential functional expression and taxonomic abundance</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        @MAKE_SAMPS_TSV@
+        metaquantome stat
+        --samps samp_file.tab
+        --mode '$mode'
+        --ontology '$ontology'
+        --file '$file'
+        --parametric '$parametric'
+        $paired
+        --outfile='$outfile'
+    ]]></command>
+    <inputs>
+        <expand macro="SAMPS"/>
+        <param argument="--file" type="data" format="tabular" label="metaquantome expanded or filtered file"
+                    help=""/>
+        <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>
+        <param name="ontology" type="select" label="Ontology">
+            <option value="go">Gene Ontology (column named 'go')</option>
+            <option value="ec">Gene Ontology (column named 'go')</option>
+            <option value="cog">COG (column named 'cog')</option>
+        </param>
+        <param argument="--parametric" type="select" label="Statistical test to perform">
+            <option value="False" selected="true">Wilcoxon test (nonparametric)</option>
+            <option value="True">standard t-test (parametric)</option>
+        </param>
+        <param argument="--paired" type="boolean" truevalue="--paired" falsevalue="" checked="false" label="Perform paired tests"/>
+        <expand macro="output_samples_choice"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="outfile" label="${tool.name} on ${on_string} stats"/>
+        <expand macro="output_samples"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="file" value="ec_ttest.tab" ftype="tabular" />
+            <param name="parametric" value="True" />
+            <param name="ontology" value="ec" />
+            <param name="mode" value="f" />
+            <output name="outfile" value="ec_ttest_tested.tab" ftype="tabular"/>
+            <!-- stat(expandfile, sinfo=TTEST_SINFO, paired=False, parametric=True, ontology='ec', mode='f',
+                      outfile=tested_file) -->
+            <param name="samps_src" value="build" />
+            <repeat name="samps">
+                <param name="group_name" value="s1"/>
+                <param name="col_names" value="int1,int2,int3"/>
+            </repeat>
+            <repeat name="samps">
+                <param name="group_name" value="s2"/>
+                <param name="col_names" value="int4,int5,int6"/>
+            </repeat>
+        </test>
+    </tests>
+    <help><![CDATA[
+        help
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff -r 000000000000 -r b17b03126d40 metaquantome_viz.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaquantome_viz.xml	Tue Dec 04 17:17:41 2018 -0500
@@ -0,0 +1,148 @@
+<tool id="metaquantome_viz" name="MetaQuantome Visualization Plots" version="@VERSION@.0">
+    <description>of taxonomic analysis, functional analysis, and function-taxonomy</description>
+    <macros>
+        <import>macros.xml</import>
+        <xml name="img_size">
+            <param argument="--height" type="float" value="" optional="true" label="Image height in inches"/>       
+            <param argument="--width" type="float" value="" optional="true" label="Image width in inches"/>       
+        </xml>
+        <xml name="common_bar_params">
+                <param argument="--meancol" type="text" label="Mean intensity column name"
+                        help="Mean intensity column name for desired experimental condition">
+                        <validator type="empty_field"/>
+                </param>
+                <param argument="--nterms" type="integer" value="5" min="1" label="Number of taxa or functional terms to display"/>
+                <param argument="--barcolor" type="integer" value="1" min="1" max="6" label="Color for the bar fill">
+                    <help>
+                        The color vector in R is
+                        c("dodgerblue", "darkorange", "yellow2", "red2", "darkviolet", "black"), 
+                        so providing a 1 will give the "dodgerblue" color. 
+                        These same colors are also used in the heatmap and PCA plot, 
+                        so the colors can be tweaked to match.
+                    </help>
+                </param>
+        </xml>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        @MAKE_SAMPS_TSV@
+        metaquantome viz
+        @COMMON_PARAMS@
+        --infile='$infile'
+        --plottype=$plot.plottype
+        #if $plot.plottype == 'bar':
+            --meancol='$plot.meancol'
+            --nterms=$plot.nterms
+            --barcolor=$plot.barcolor
+        #elif $plot.plottype == 'volcano':
+            --fc='$plot.fc'
+            #if $plot.textannot:
+                --textannot='$plot.textannot'
+            #end if
+            $plot.gosplit
+        #elif $plot.plottype == 'heatmap':
+            $plot.filter_to_sig
+            --alpha=$plot.alpha
+        #elif $plot.plottype == 'pca':
+            $plot.calculate_sep
+        #elif $plot.plottype == 'ft_dist':
+            --meancol='$plot.meancol'
+            --nterms=$plot.nterms
+            --barcolor=$plot.barcolor
+            --whichway=$plot.whichway
+            #if $plot.term.id_or_name == 'id':
+                --id='$plot.term.id'
+            #else:
+                --name='$plot.term.name'
+            #end if
+            #if $plot.target_onto:
+                --target_onto=$plot.target_onto
+            #end if
+        #end if
+        #if $plot.height:
+            --height=$plot.height
+        #end if
+        #if $plot.width1:
+            --width=$plot.width
+        #end if
+        --img='outfile.png'
+    ]]></command>
+    <inputs>
+        <expand macro="common_params"/>
+        <param argument="--infile" type="data" format="tabular" label="metaquantome stats or filtered file"
+                    help=""/>
+        <conditional name="plot">
+            <param argument="--plottype" type="select" label="Plot type">
+                <option value="bar">Bar Chart</option>
+                <option value="volcano">Volcano Plot</option>
+                <option value="heatmap">Heatmap</option>
+                <option value="pca">PCA - Principal Componets Analysis</option>
+                <option value="ft_dist">Bar Chart</option>
+            </param>
+            <when value="bar">
+                <expand macro="common_bar_params"/>
+                <expand macro="img_size"/>
+            </when>
+            <when value="volcano">
+                <param argument="--fc" type="text" label="Name of the fold change column in the stat dataframe">
+                        <validator type="empty_field"/>
+                </param>
+                <param argument="--textannot" type="text" optional="true" label="Name of the annotation column" 
+                    help="Provides text annoatation for the plot.  Optional, if missing, no text will be plotted."/>
+                <param argument="--gosplit" type="boolean" truevalue="--gosplit" falsevalue="" checked="false" 
+                    label="Make one plot for each of BiologicalProcess, CellularComponent, and MolecularFunction"/>
+                <expand macro="img_size"/>
+            </when>
+            <when value="heatmap">
+                <param argument="--filter_to_sig" type="boolean" truevalue="--filter_to_sig" falsevalue="" checked="false" 
+                    label="Only plot significant term" help="Necessitates use of results from `test`"/>
+                <param argument="--aplha" type="float" value="0.05" min="0.0" max="1.0" label="If filter_to_sig, the q-value significance level"/>
+                <expand macro="img_size"/>
+            </when>
+            <when value="pca">
+                <param argument="--calculate_sep" type="boolean" truevalue="--calculate_sep" falsevalue="" checked="false" 
+                    label="Calculate separation between groups and include in title"/>
+                <expand macro="img_size"/>
+            </when>
+            <when value="ft_dist">
+                <expand macro="common_bar_params"/>
+                <param argument="--whichway" type="select" label="which distribution">
+                    <option value="f_dist">functional distribution for a taxon</option>
+                    <option value="t_dist">taxonomic distribution for a function</option>
+                </param>
+                <conditional name="term">
+                    <param argument="id_or_name" type="select" label="">
+                        <option value="id">Taxonomic or functional term ID</option>
+                        <option value="name">Taxonomic or functional term name</option>
+                    </param>
+                    <when value="id">
+                        <param argument="--id" type="text" label="Taxonomic or functional term id">
+                            <help>
+                                NCBI taxID or a GO term id (GO:XXXXXXX)
+                            </help>
+                        </param>
+                    </when>
+                    <when value="name">
+                       <param argument="--name" type="text" label="Taxonomic or functional term name">
+                           <help>
+                           </help>
+                       </param>
+                    </when>
+                </conditional>
+                <param argument="--target_onto" type="select" optional="true" label="Restrict to GO category">
+                    <option value="bp">Biological Process</option>
+                    <option value="mf">Molecular Function</option>
+                    <option value="cc">Cellular Component</option>
+                </param>
+                <expand macro="img_size"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="png" name="outfile" label="${tool.name} on ${on_string} ${plot.plottype}" from_work_dir="outfile.png"/>
+    </outputs>
+    <help><![CDATA[
+        TODO: Fill in help.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff -r 000000000000 -r b17b03126d40 test-data/ec_ttest.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ec_ttest.tab	Tue Dec 04 17:17:41 2018 -0500
@@ -0,0 +1,8 @@
+id	description	s1_mean	s2_mean	int1	int2	int3	int4	int5	int6	int1_n_peptide	int2_n_peptide	int3_n_peptide	int4_n_peptide	int5_n_peptide	int6_n_peptide	int1_n_samp_children	int2_n_samp_children	int3_n_samp_children	int4_n_samp_children	int5_n_samp_children	int6_n_samp_children
+1.-.-.-	Oxidoreductases.	10.013089999440444	3.5443205162238103	9.965784284662087	10.228818690495881	9.813781191217037	3.584962500721156	3.700439718141092	3.321928094887362	1	1	1	1	1	1	1.0	1.0	1.0	1.0	1.0	1.0
+1.2.-.-	Acting on the aldehyde or oxo group of donors.	10.013089999440444	3.5443205162238103	9.965784284662087	10.228818690495881	9.813781191217037	3.584962500721156	3.700439718141092	3.321928094887362	1	1	1	1	1	1	NA	NA	NA	NA	NA	NA
+3.-.-.-	Hydrolases.	5.285402218862249	11.475564566327487	5.0	5.643856189774724	5.129283016944966	11.778077129535358	10.980853606379736	11.555547771647065	2	2	2	2	2	2	1.0	1.0	1.0	1.0	1.0	1.0
+3.4.-.-	Acting on peptide bonds (peptidases).	5.285402218862249	11.475564566327487	5.0	5.643856189774724	5.129283016944966	11.778077129535358	10.980853606379736	11.555547771647065	2	2	2	2	2	2	2.0	2.0	2.0	2.0	2.0	2.0
+3.4.11.-	Aminopeptidases.	3.969626350956481	3.841302253980942	3.584962500721156	4.321928094887363	3.9068905956085187	3.584962500721156	4.392317422778761	3.321928094887362	1	1	1	1	1	1	NA	NA	NA	NA	NA	NA
+3.4.21.-	Serine endopeptidases.	4.54432051622381	11.46828462519127	4.321928094887363	4.906890595608519	4.321928094887363	11.77313920671969	10.965784284662087	11.550746785383243	1	1	1	1	1	1	1.0	1.0	1.0	1.0	1.0	1.0
+3.4.21.70	Pancreatic endopeptidase E.	4.54432051622381	11.46828462519127	4.321928094887363	4.906890595608519	4.321928094887363	11.77313920671969	10.965784284662087	11.550746785383243	1	1	1	1	1	1	NA	NA	NA	NA	NA	NA
diff -r 000000000000 -r b17b03126d40 test-data/ec_ttest_tested.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ec_ttest_tested.tab	Tue Dec 04 17:17:41 2018 -0500
@@ -0,0 +1,8 @@
+id	description	s1_mean	s2_mean	int1	int2	int3	int4	int5	int6	int1_n_peptide	int2_n_peptide	int3_n_peptide	int4_n_peptide	int5_n_peptide	int6_n_peptide	int1_n_samp_children	int2_n_samp_children	int3_n_samp_children	int4_n_samp_children	int5_n_samp_children	int6_n_samp_children	log2fc_s1_over_s2	p	corrected_p
+1.-.-.-	Oxidoreductases.	10.013089999440444	3.5443205162238103	9.965784284662089	10.228818690495881	9.813781191217037	3.584962500721156	3.700439718141092	3.3219280948873617	1.0	1.0	1.0	1.0	1.0	1.0	1.0	1.0	1.0	1.0	1.0	1.0	6.468769483216634	2.70286875006428e-06	9.46004062522498e-06
+1.2.-.-	Acting on the aldehyde or oxo group of donors.	10.013089999440444	3.5443205162238103	9.965784284662089	10.228818690495881	9.813781191217037	3.584962500721156	3.700439718141092	3.3219280948873617	1.0	1.0	1.0	1.0	1.0	1.0	NA	NA	NA	NA	NA	NA	6.468769483216634	2.70286875006428e-06	9.46004062522498e-06
+3.-.-.-	Hydrolases.	5.28540221886225	11.475564566327488	5.0	5.6438561897747235	5.1292830169449655	11.778077129535358	10.980853606379736	11.555547771647065	2.0	2.0	2.0	2.0	2.0	2.0	1.0	1.0	1.0	1.0	1.0	1.0	-6.190162347465239	4.742887028677606e-05	5.533368200123874e-05
+3.4.-.-	Acting on peptide bonds (peptidases).	5.28540221886225	11.475564566327488	5.0	5.6438561897747235	5.1292830169449655	11.778077129535358	10.980853606379736	11.555547771647065	2.0	2.0	2.0	2.0	2.0	2.0	2.0	2.0	2.0	2.0	2.0	2.0	-6.190162347465239	4.742887028677606e-05	5.533368200123874e-05
+3.4.11.-	Aminopeptidases.	3.9696263509564815	3.841302253980942	3.584962500721156	4.3219280948873635	3.906890595608519	3.584962500721156	4.392317422778762	3.3219280948873617	1.0	1.0	1.0	1.0	1.0	1.0	NA	NA	NA	NA	NA	NA	0.1283240969755397	0.6832561051460733	0.6832561051460733
+3.4.21.-	Serine endopeptidases.	4.544320516223809	11.468284625191268	4.3219280948873635	4.906890595608519	4.3219280948873635	11.773139206719689	10.965784284662087	11.550746785383243	1.0	1.0	1.0	1.0	1.0	1.0	1.0	1.0	1.0	1.0	1.0	1.0	-6.923964108967459	3.349508567404191e-05	5.533368200123874e-05
+3.4.21.70	Pancreatic endopeptidase E.	4.544320516223809	11.468284625191268	4.3219280948873635	4.906890595608519	4.3219280948873635	11.773139206719689	10.965784284662087	11.550746785383243	1.0	1.0	1.0	1.0	1.0	1.0	NA	NA	NA	NA	NA	NA	-6.923964108967459	3.349508567404191e-05	5.533368200123874e-05
diff -r 000000000000 -r b17b03126d40 test-data/go_expanded.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/go_expanded.tab	Tue Dec 04 17:17:41 2018 -0500
@@ -0,0 +1,6 @@
+id	name	namespace	s1_mean	s2_mean	int1	int2	int3	int4	int5	int6	int1_n_peptide	int2_n_peptide	int3_n_peptide	int4_n_peptide	int5_n_peptide	int6_n_peptide	int1_n_samp_children	int2_n_samp_children	int3_n_samp_children	int4_n_samp_children	int5_n_samp_children	int6_n_samp_children
+GO:0000003	reproduction	biological_process	10.013089999440444	3.5443205162238103	9.965784284662087	10.228818690495881	9.813781191217037	3.584962500721156	3.700439718141092	3.321928094887362	1	1	1	1	1	1	1.0	1.0	1.0	1.0	1.0	1.0
+GO:0008150	biological_process	biological_process	10.066537719931583	11.4814630999144	10.011227255423254	10.287712379549449	9.868822554774999	11.782998208920414	10.9901039638575	11.560332834212442	3	3	3	3	3	3	3.0	3.0	3.0	3.0	3.0	3.0
+GO:0008152	metabolic process	biological_process	3.969626350956481	3.841302253980942	3.584962500721156	4.321928094887363	3.9068905956085187	3.584962500721156	4.392317422778761	3.321928094887362	1	1	1	1	1	1	NA	NA	NA	NA	NA	NA
+GO:0022610	biological adhesion	biological_process	4.54432051622381	11.46828462519127	4.321928094887363	4.906890595608519	4.321928094887363	11.77313920671969	10.965784284662087	11.550746785383243	1	1	1	1	1	1	NA	NA	NA	NA	NA	NA
+GO:0032505	reproduction of a single-celled organism	biological_process	10.013089999440444	3.5443205162238103	9.965784284662087	10.228818690495881	9.813781191217037	3.584962500721156	3.700439718141092	3.321928094887362	1	1	1	1	1	1	NA	NA	NA	NA	NA	NA
diff -r 000000000000 -r b17b03126d40 test-data/int_ttest.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/int_ttest.tab	Tue Dec 04 17:17:41 2018 -0500
@@ -0,0 +1,4 @@
+peptide	int1	int2	int3	int4	int5	int6
+A	12	20	15	12	21	10
+B	20	30	20	3500	2000	3000
+C	1000	1200	900	12	13	10
diff -r 000000000000 -r b17b03126d40 test-data/multiple_func.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_func.tab	Tue Dec 04 17:17:41 2018 -0500
@@ -0,0 +1,4 @@
+peptide	cog	go
+A	C	GO:0008152
+B	N	GO:0022610
+C	D	GO:0000003,GO:0032505
diff -r 000000000000 -r b17b03126d40 test-data/multiple_int.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_int.tab	Tue Dec 04 17:17:41 2018 -0500
@@ -0,0 +1,4 @@
+peptide	int1	int2	int3
+A	10	20	70
+B	40	30	30
+C	50	50	0
diff -r 000000000000 -r b17b03126d40 test-data/multiple_tax.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_tax.tab	Tue Dec 04 17:17:41 2018 -0500
@@ -0,0 +1,4 @@
+peptide	lca
+A	210
+B	1496
+C	1870884