diff gemini_amend.xml @ 0:ccd8fdcf82d1 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_amend.xml	Thu Feb 18 08:54:53 2016 -0500
@@ -0,0 +1,70 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>Amend an already loaded GEMINI database.</description>
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">amend</token>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+        cp "${ infile }" "${ outfile }" &&
+
+        gemini @BINARY@
+        $clear
+        --sample "${ ped }"
+
+        "${ outfile }"
+]]>
+    </command>
+    <inputs>
+
+        <expand macro="infile" />
+        <param name="ped" type="data" format="tabular" optional="True" label="Additional sample information file in PED+ format" help="(--sample)" />
+        <param argument="--clear" type="boolean" truevalue="--clear" falsevalue="" checked="False" label="Set all values to None before loading" help="Makes it possible to delete values. Otherwise the old ones are kept"/>
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="gemini.sqlite" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" />
+            <param name="ped" value="gemini_amend_input.ped" ftype="tabular" />
+            <output name="outfile" file="gemini_amend_result.db" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Gemini amend adds information about the samples via PED file.
+
+If you have a sample table in a Gemini db that looks like this::
+
+ sample_id   family_id   name      paternal_id   maternal_id   sex   phenotype   hair_color   
+ 1           1           M10475    0             0             1     1           brown        
+ 2           1           M10478    M10475        M10500        2     2           blonde       
+ 3           1           M10500    0             0             2     2           purple       
+
+and you want the change the haircolor of sample 3. And also add some information about the preferred hobbies of some samples.
+
+You could specify the following PED file. ::
+
+ #family_id  name    paternal_id  maternal_id  sex  phenotype  hair_color  hobby
+ 1           M10475  None         None         1    1          brown       fishing
+ 1           M10478  M10475       M10500       2    2          red         biking
+ 1           M10500  None         None         2    2          purple 
+
+this results in::
+
+ sample_id   family_id   name      paternal_id   maternal_id   sex   phenotype   hair_color   hobby     
+ 1           1           M10475    0             0             1     1           brown        fishing   
+ 2           1           M10478    M10475        M10500        2     2           red          biking    
+ 3           1           M10500    0             0             2     2           purple       .         
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>