--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/specify.xml	Fri Sep 28 11:48:38 2012 -0400
@@ -0,0 +1,87 @@
+<tool id="gd_specify" name="Specify Individuals" version="1.0.0">
+  <description>: Define a collection of individuals from a gd_snp dataset</description>
+
+  <command interpreter="bash">
+    echo.bash "$input" "$output"
+    #for $individual in str($individuals).split(',')
+        #set $individual_idx = $input.dataset.metadata.individual_names.index($individual)
+        #set $individual_col = str( $input.dataset.metadata.individual_columns[$individual_idx] )
+        #set $arg = '\t'.join([$individual_col, $individual, ''])
+        "$arg"
+    #end for
+  </command>
+
+  <inputs>
+    <param name="input" type="data" format="gd_snp" label="SNP dataset"/>
+    <param name="individuals" type="select" display="checkboxes" multiple="true" label="Individuals to include">
+      <options>
+        <filter type="data_meta" ref="input" key="individual_names" />
+      </options>
+      <validator type="no_options" message="You must select at least one individual."/>
+    </param>
+    <param name="outname" type="text" size="20" label="Label for this collection">
+      <validator type="empty_field" message="You must enter a label."/>
+      #used to be "Individuals from ${input.hid}"
+    </param>
+  </inputs>
+
+  <outputs>
+    <data name="output" format="gd_indivs" label="${outname}" />
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
+      <param name="individuals" value="PB1,PB2" />
+      <output name="output" file="test_in/a.gd_indivs" />
+    </test>
+  </tests>
+
+  <help>
+
+**Dataset formats**
+
+The input dataset is in gd_snp_ format;
+the output is in gd_indivs_ format.  (`Dataset missing?`_)
+
+.. _gd_snp: ./static/formatHelp.html#gd_snp
+.. _gd_indivs: ./static/formatHelp.html#gd_indivs
+.. _Dataset missing?: ./static/formatHelp.html
+
+-----
+
+**What it does**
+
+This tool makes a list of selected entities (the sets of four columns
+representing individuals or groups) from a gd_snp dataset.  It does not copy
+the SNP data; it just records which entities should be considered as belonging
+to some collection or population.  The label you specify is used to name the
+output dataset in your history.  This list can then be used to instruct other
+tools to work on just part of the original gd_snp dataset.
+
+-----
+
+**Example**
+
+- input::
+
+   Contig161_chr1_4641264_4641879   115  C  T  73.5   chr1   4641382  C   6  0  2  45   8  0  2  51   15  0  2  72   5  0  2  42   6  0  2  45  10  0  2  57   Y  54  0.323  0
+   Contig48_chr1_10150253_10151311   11  A  G  94.3   chr1  10150264  A   1  0  2  30   1  0  2  30    1  0  2  30   3  0  2  36   1  0  2  30   1  0  2  30   Y  22  +99.   0
+   Contig20_chr1_21313469_21313570   66  C  T  54.0   chr1  21313534  C   4  0  2  39   4  0  2  39    5  0  2  42   4  0  2  39   4  0  2  39   5  0  2  42   N   1  +99.   0
+   etc.
+
+- input metadata::
+
+   #{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc",
+   #"1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q",
+   #"pair","dist","prim","rflp"],"dbkey":"canFam2","individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],
+   #"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"}
+
+- output when individuals PB1, PB2, and PB3 are selected::
+
+   9   PB1
+   13  PB2
+   17  PB3
+
+  </help>
+</tool>