diff metaquantome_expand.xml @ 0:170b5fa2402d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaquantome_expand.xml	Thu Apr 25 13:46:17 2019 -0400
@@ -0,0 +1,234 @@
+<tool id="metaquantome_expand" name="metaQuantome: expand" version="@GVERSION@">
+  <description>a set of functional or taxonomy annotations</description>
+  <macros>
+    <import>macros.xml</import>
+    <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 with GO terms, EC number, or COG."/>
+      <param argument="--pep_colname_func" type="text" label="Functional file: peptide column name" value="peptide"
+          help="The column name within the function file that corresponds to the peptide sequences">
+          <validator type="empty_field"/>
+      </param>
+    </xml>
+    <xml name="FUNC_COLNAME">
+      <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="Taxonomy file: peptide column name" value="peptide"
+          help="The column name within the taxonomy file that corresponds to the peptide sequences">
+          <validator type="empty_field"/>
+      </param>
+    </xml>
+    <xml name="TAX_COLNAME">
+      <param argument="--tax_colname" type="text" label="Taxonomy column name">
+          <help>
+              Name of column in taxonomy annotation file that contains
+              the lowest common ancestor (LCA) annotation. The annotations must
+              be either NCBI taxids (strongly preferred) or taxonomy
+              names.
+          </help>
+          <validator type="empty_field"/>
+      </param>
+    </xml>
+    <xml name="FT_TAR_RANK">
+      <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>
+    </xml>
+    <token name="@FUNC_FILE@">
+      --func_file='$mode_args.func_file'
+      --pep_colname_func='$mode_args.pep_colname_func'
+    </token>
+    <token name="@FUNC_COLNAME@">
+      --func_colname='$mode_args.func_colname'
+    </token>
+    <token name="@ONTOLOGY@">
+      --ontology='$mode_args.ontology_args.ontology'
+      #if $mode_args.ontology_args.ontology == 'go'
+          #if $mode_args.ontology_args.slim_down
+              --slim_down
+          #end if
+      #end if
+    </token>
+    <token name="@TAX_FILE@">
+      --tax_file='$mode_args.tax_file'
+      --pep_colname_tax='$mode_args.pep_colname_tax'
+    </token>
+    <token name="@TAX_COLNAME@">
+      --tax_colname='$mode_args.tax_colname'
+    </token>
+    <token name="@FT_TAR_RANK@">
+      --ft_tar_rank='$mode_args.ft_tar_rank'
+    </token>
+  </macros>
+  <expand macro="requirements" />
+  <command detect_errors="exit_code"><![CDATA[
+    tar -xf '$db_tar' &&
+    metaquantome expand
+    --data_dir ./data
+    --samps '$samps'
+    --mode '$mode_args.mode'
+    --int_file='$int_file'
+    --pep_colname_int='$pep_colname_int'
+    #if $mode_args.mode == 'f'
+      @FUNC_FILE@
+      @FUNC_COLNAME@
+      @ONTOLOGY@
+    #elif $mode_args.mode =='t'
+      @TAX_FILE@
+      @TAX_COLNAME@
+    #elif $mode_args.mode == 'ft'
+      @FUNC_FILE@
+      @FUNC_COLNAME@
+      @ONTOLOGY@
+      @TAX_FILE@
+      @TAX_COLNAME@
+      @FT_TAR_RANK@
+    #end if
+    --outfile='$outfile'
+  ]]></command>
+  <inputs>
+    <param name="db_tar" type="data" format="tar" label="Database Archive File"
+      help="must be created by 'metaQuantome: download'"/>
+    <expand macro="SAMPS"/>
+      <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"/>
+          <expand macro="ONTOLOGY_ARGS"/>
+          <expand macro="FUNC_COLNAME"/>
+        </when>
+        <when value="t">
+          <expand macro="TAX_FILE"/>
+          <expand macro="TAX_COLNAME"/>
+        </when>
+        <when value="ft">
+          <expand macro="FUNC_FILE"/>
+          <expand macro="FUNC_COLNAME"/>
+          <expand macro="ONTOLOGY_ARGS"/>
+          <expand macro="TAX_FILE"/>
+          <expand macro="TAX_COLNAME"/>
+          <expand macro="FT_TAR_RANK"/>
+        </when>
+      </conditional>
+      <param argument="--int_file" type="data" format="tabular" label="Intensity file"
+        help=""/>
+      <param argument="--pep_colname_int" type="text" value="peptide" label="Intensity file: peptide column name"
+        help="The column name within the intensity file that corresponds to the peptide sequences">
+        <validator type="empty_field"/>
+      </param>
+  </inputs>
+  <outputs>
+      <data format="tabular" name="outfile" label="${tool.name} on ${on_string} expanded"/>
+  </outputs>
+  <tests>
+    <test>
+       <param name="db_tar" value="ec.tar" ftype="tar"/>
+       <param name="samps" value="samples_basic.tab" ftype="tabular"/>
+       <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="ec"/>
+       <param name="mode" value="f" />
+       <param name="ontology" value="ec" />
+       <output name="outfile">
+         <assert_contents>
+           <has_text text="1.2.7.10"/>
+         </assert_contents>
+       </output>
+    </test>
+  </tests>
+  <help>
+<![CDATA[
+metaQuantome expand
+===================
+
+The *expand* module is the first analysis step in the metaQuantome analysis workflow,
+and can be run to analyze function, taxonomy, or function and taxonomy together.
+
+To prepare to run this module, you must create your samples file with
+"metaQuantome: create samples file" and download the necessary databases with
+"metaQuantome: database".
+
+Some example analysis workflows are:
+
+1. Get the functional, taxonomic, or functional-taxonomic distribution: run expand, filter, and viz.
+2. Cluster analysis: run expand, filter, and viz. The viz module has heatmaps and PCA plots for cluster analysis.
+3. Differential expression: run expand, filter, stat, and viz.
+
+
+The following information is required for all 3 analysis modes
+(function, taxonomy, and function-taxonomy).
+
+- experimental design information.
+- a tab-separated peptide intensity file.
+- the name of the peptide column in the intensity file.
+
+Function mode
+-------------
+
+In function mode, the following information is required:
+
+- the ontology being used: Gene Ontology (GO), Clusters of Orthologous Groups (COG), or Enzyme Commission (EC) numbers.
+- a tab-separated functional annotation file, with a peptide column and a functional annotation column. An entry in the functional annotation column may contain multiple functional annotations separated by commas.
+- the name of the peptide column in the functional annotation file.
+- the name of the functional annotation column in the functional annotation file.
+
+Taxonomy mode
+-------------
+
+In taxonomy mode, the following information is required:
+
+- a tab-separated taxonomy annotation file, with a peptide column and a taxonomy annotation column. The taxonomic annotations should be the lowest common ancestor (LCA) for each peptide, preferably given as NCBI taxonomy IDs.
+- the name of the peptide column in the taxonomic annotation file.
+- the name of the taxonomy annotation column in the taxonomy annotation file.
+
+Function-Taxonomy mode
+----------------------
+
+In the combined mode, all of the above must be provided. In addition, the "target rank" must be provided, which is the desired taxonomic rank at which to summarize the function/taxonomy results.
+
+Output of the expand module
+---------------------------
+
+The structure of the output file depends on the analysis mode and the experimental design,
+but the columns generally look like this, with one row for each term:
+
+=======  =======================  =======================  ======================  =========================  ==========================
+term id  info about term.         mean term intensity      term intensity          number of unique peptides  number of sample children
+         (one or more columns)    (by sample group)        (by sample)             (by sample)                in each sample
+=======  =======================  =======================  ======================  =========================  ==========================
+term1    name, rank, etc.         note that this           this is the log2        integer. 0 is coded as NA  integer. 0 is coded as NA
+                                  is the log2 of the mean  of term intensity
+                                  intensity                in each sample.
+                                                           Missing data is coded
+                                                           as NA.
+=======  =======================  =======================  ======================  =========================  ==========================
+
+The next step in the metaQuantome workflow is "filter", which
+filters out rows that don't meet certain conditions on the intensity,
+the number of unique peptides annotated with each term, and the
+number of sample children.
+
+Questions, Comments, Problems, Kudos
+------------------------------------
+
+Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
+]]></help>
+  <expand macro="citations" />
+</tool>