diff obistat.xml @ 0:ee9cd37c2f3d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/obistat.xml	Wed Apr 12 17:38:35 2017 -0400
@@ -0,0 +1,138 @@
+<tool id="obi_stat" name="obistat" version="@WRAPPER_VERSION@">
+    <description>computes basic statistics for attribute values</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <command>
+
+        <![CDATA[
+
+        obistat
+        #for $attribute in $catattributes
+            #if str( $attribute.options_attributespe.options_attributespe_selector) == "key"
+                -c '$attribute.options_attributespe.options_catattribute_selector'
+            #end if
+            #if str( $attribute.options_attributespe.options_attributespe_selector) == "python"
+                -c '${attribute.options_attributespe.attribute}'
+            #end if
+        #end for
+
+        #if str( $options_attribute.options_attributebe_selector) == "yes"
+            #if str( $options_attribute.options_attribute_selector) == "min"
+                -m '$options_attribute.options_uniq_selector'
+            #end if
+            #if str( $options_attribute.options_attribute_selector) == "max"
+                -M '$options_attribute.options_uniq_selector'
+            #end if
+            #if str( $options_attribute.options_attribute_selector) == "mean"
+                -a '$options_attribute.options_uniq_selector'
+            #end if
+            #if str( $options_attribute.options_attribute_selector) == "variance"
+                -v '$options_attribute.options_uniq_selector'
+            #end if
+            #if str( $options_attribute.options_attribute_selector) == "std"
+                -s '$options_attribute.options_uniq_selector'
+            #end if
+        #end if
+
+        '$input' > '$output'
+
+        ]]>
+
+
+    </command>
+
+    <inputs>
+        <param name="input" type="data" format="fasta,fastq" label="Input sequences file" />
+
+        <repeat name="catattributes" title="Category attribute" min="0">
+            <conditional name="options_attributespe">
+                <param name="options_attributespe_selector" type="select" label="How would you specify the category attribute key?" >
+                    <option value="key" selected="true">simply by a key of an attribute</option>
+                    <option value="python">by a python expression</option>
+                </param>
+                <when value="python">
+                    <param name="attribute" type="text" label="Regular expression pattern matched against the attributes of the sequence record. the value of this attribute is of the form : key:regular_pattern. The pattern is case sensitive." >
+                        <expand macro="sanitizer"/>
+                    </param>
+                </when>
+                <when value="key">
+                    <param name="options_catattribute_selector" type="select" label="Attribute used to categorize the sequence records" >
+                        <expand macro="attributes"/>
+                    </param>
+                </when>
+            </conditional>
+        </repeat>
+
+        <conditional name="options_attribute">
+            <param name="options_attributebe_selector" type="select" label="Use a specific option" >
+                <option value="None" selected="true">no</option>
+                <option value="yes">yes</option>
+            </param>
+            <when value="yes">
+                <param name="options_attribute_selector" type="select" label="Select your specific option" >
+                    <option value="min" selected="true">min</option>
+                    <option value="max">max</option>
+                    <option value="mean">mean</option>
+                    <option value="variance">variance</option>
+                    <option value="std">standard deviation</option>
+                </param>
+                <param name="options_uniq_selector" type="select" label="Attribute to merge" >
+                    <expand macro="attributes"/>
+                </param>
+            </when>
+            <when value="None"></when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="txt" name="output" label="output.txt with ${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="output_obiannotate.fasta" />
+            <conditional name="catattributes_0|options_attributespe">
+                <param name="options_attributespe_selector" value="key"/>
+                <param name="options_catattribute_selector" value="count" />
+            </conditional>
+            <conditional name="catattributes_1|options_attributespe">
+                <param name="options_attributespe_selector" value="key"/>
+                <param name="options_catattribute_selector" value="merged" />
+            </conditional>
+            <conditional name="options_attribute">
+                <param name="options_attributebe_selector" value="yes"/>
+                <param name="options_attribute_selector" value="min" />
+                <param name="options_uniq_selector" value="seq_length" />
+            </conditional>
+
+            <output name="output" file="output_obistat.txt" ftype="txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+stats computes basic statistics for attribute values of sequence records. The sequence records can be categorized or not using one or several -c options. By default, only the number of sequence records and the total count are computed for each category. Additional statistics can be computed for attribute values in each category, like:
+
+\*  minimum value (-m option)
+
+\*  maximum value (-M option)
+
+\*  mean value (-a option)
+
+\*  variance (-v option)
+
+\*  standard deviation (-s option)
+
+The result is a contingency table with the different categories in rows, and the computed statistics in columns.
+
+@OBITOOLS_LINK@
+
+        ]]>
+    </help>
+    <expand macro="citation" />
+</tool>