diff metaquantome_sample.xml @ 5:5bc492a15b8b draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaquantome_sample.xml	Thu Feb 07 17:54:28 2019 -0500
@@ -0,0 +1,117 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool id="sample" name="metaQuantome: create samples file" version="@VERSION@.3">
+    <description></description>
+    <macros>
+        <token name="@VERSION@">1.1.2</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">megahit</requirement>
+    </requirements>
+    <version_command>megahit --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        #set $samp_header = 'group\tcolnames'
+        echo -e '${samp_header}' > samp_file.tab;
+        #if $samps_args.samps_src == 'build':
+            #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
+        #else:
+            #for $s in $samps_args.samps
+                cat ${samps_args.file} | cut -f ${s.col_names} |
+                head -n 1 | tr '\t' ',' |
+                cat <(echo -e -n "${s.group_name}\t") - >> samp_file.tab;
+            #end for
+        #end if
+    ]]></command>
+    <inputs>
+        <conditional name="samps_args">
+            <param name="samps_src" type="select" label="Sample file creation method">
+                <option value="build">Specify samples</option>
+                <option value="history">Select samples from existing file's header</option>
+            </param>
+            <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" help="Specify the column names of the sample file. Use commas to separate multiple columns." />
+                </repeat>
+            </when>
+            <when value="history">
+                <param name="file" type="data" format="tabular" label="File with group name headers" help="Ex: moFF tool output (headers: peptide X737NS X737WS)" />
+                <repeat name="samps" title="Samples">
+                    <param name="group_name" type="text" label="Group name" />
+                    <param name="col_names" type="data_column" multiple="true" data_ref="file" label="Column" help="Specify the column indices of the file's header" />
+                </repeat>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="samples_file" from_work_dir="samp_file.tab" label="${tool.name}  ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="samps_src" value="build" />
+            <repeat name="samps">
+                <param name="group_name" value="NS"/>
+                <param name="col_names" value="X737NS,X852NS,X867NS"/>
+            </repeat>
+            <repeat name="samps">
+                <param name="group_name" value="WS"/>
+                <param name="col_names" value="X737WS,X852WS,X867WS"/>
+            </repeat>
+            <output name="samples_file" file="samples.tab" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="samps_src" value="history" />
+            <param name="file" value="int_737_test.tab" ftype="tabular" />
+            <repeat name="samps">
+                <param name="group_name" value="NS"/>
+                <param name="col_names" value="3,5,7"/>
+            </repeat>
+            <repeat name="samps">
+                <param name="group_name" value="WS"/>
+                <param name="col_names" value="2,4,6"/>
+            </repeat>
+            <output name="samples_file" file="samples.tab" ftype="tabular" />
+        </test>
+    </tests>
+    <help><![CDATA[
+metaQuantome: create samples file
+===================
+
+The *create samples file* module is used to generate the *samples file* input file for the metaQuantome workflow. This input file is used to specify which column names are affilated with which experimental groups. 
+
+*Create samples file*
+
+    =====  ====================
+    group  colnames   
+    =====  ====================
+    NS     X737NS,X852NS,X867NS  
+    WS     X737WS,X852WS,X867WS
+    =====  ==================== 
+
+
+There are two methods for generating this input file:
+
+1. **Specify Samples** You may specify the samples by providing the group names (ex: NS *no sucrose* and WS *with sucrose*) and each of their affilated column names (ex: X737WS, X737NS, etc...) from the input files (e.g., peptide intensity *int.tab*). 
+
+2. **Select samples from existing file's header** Alternatively, you can indicate the column indices of the selected headers for each experimental group (ex: columns 1, 3, and 5 for NS; columns 2, 4, and 6 for WS). You need to specify which file from the history you are referencing. An example is shown below.
+
+*Example int.tab file*
+============ ====== ======  ======  ======  ======  ====== 
+peptide      X737WS X737NS  X852WS  X852NS  X867WS  X867NS
+============ ====== ======  ======  ======  ======  ======
+LPGQQHGTPSAK 1      2       3       4       5       6
+ELPGLAALTDK  7      8       9       10      11      12
+============ ====== ======  ======  ======  ======  ======
+
+
+Questions, Comments, Problems, Kudos
+------------------------------------
+
+Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btv033</citation>
+    </citations>
+</tool>