bamtools_filter: bamtools-filter.xml comparison

comparison bamtools-filter.xml @ 2:2098a49ddf66 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7

author	devteam
date	Wed, 11 Nov 2015 12:33:46 -0500
parents	d64c7e752f4d
children	29ba2103739c

comparison

equal deleted inserted replaced

-:d64c7e752f4d
+:2098a49ddf66
-<tool id="bamFilter" name="Filter" version="0.0.1">
+<tool id="bamFilter" name="Filter" version="0.0.2">
 <description>BAM datasets on a variety of attributes</description>
 <requirements>
 <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement>
 </requirements>
 <command>
 cat $script_file > $out_file2;
 #for $bam_count, $input_bam in enumerate( $input_bams ):
-ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &amp;&amp;
+ln -s "${input_bam}" "localbam_${bam_count}.bam" &amp;&amp;
-ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp;
+ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp;
 #end for
 bamtools
 filter
 -script $script_file
 #for $bam_count, $input_bam in enumerate( $input_bams ):
 -in "localbam_${bam_count}.bam"
 #end for
 -out $out_file1
 </command>
 <inputs>
-<repeat name="input_bams" title="BAM dataset(s) to filter" min="1">
+<param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/>
-<param name="input_bam" type="data" format="bam" label="BAM dataset" />
-</repeat>
 <repeat name="conditions" title="Condition" min="1">
 <repeat name="filters" title="Filter" min="1">
 <conditional name="bam_property">
 <param name="bam_property_selector" type="select" label="Select BAM property to filter on">
 <option value="alignmentFlag"/>
 <!-- would be fanstastic to have AND and OR constructs in when statements -->
 <when value="alignmentFlag">
 <param name="bam_property_value" type="integer" value="3" label="Filter on this alignment flag" help="Default (3) is for a paired read mapped in a proper pair"/>
 </when>
 <when value="cigar">
-<param name="bam_property_value" type="text" size="10" value="101M" label="Filter on this CIGAR string" help="Default (101M) is for 101 continuously matched bases"/>
+<param name="bam_property_value" type="text" value="101M" label="Filter on this CIGAR string" help="Default (101M) is for 101 continuously matched bases"/>
 </when>
 <when value="insertSize">
-<param name="bam_property_value" type="text" size="10" value=">=250" label="Filter on inster size" help="You can use &gt;, &lt;, =, and ! (not) in your expression. E.g., to select pairs with inster size above 250 nt use &quot;>=250&quot;">
+<param name="bam_property_value" type="text" value=">=250" label="Filter on inster size" help="You can use &gt;, &lt;, =, and ! (not) in your expression. E.g., to select pairs with inster size above 250 nt use &quot;>=250&quot;">
 <sanitizer invalid_char="">
 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
 </sanitizer>
 </param>
 </when>
 </repeat>
 </repeat>
 <conditional name="rule_configuration">
 <param name="rules_selector" type="boolean" truevalue="true" falsevalue="false" label="Would you like to set rules?" help="Allows complex logical constructs. See Example 4 below." />
 <when value="true">
-<param name="rules" type="text" size="20" label="Enter rules here" help="This option can only be used with at least two conditions. Read help below (Example 4) to understand how it works." >
+<param name="rules" type="text" label="Enter rules here" help="This option can only be used with at least two conditions. Read help below (Example 4) to understand how it works." >
 <sanitizer invalid_char="">
 <valid initial="string.printable"/>
 </sanitizer>
 </param>
 </when>
 [
 #end if
 #for $i, $c in enumerate( $conditions, start=1 )
 { "id": "$i",
 #for $j, $s in enumerate( $c.filters, start=1 )
 ##The if below takes care of the comma at the end of last condition within group
 #if $j != len( $c.filters)
 "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}",
 #else
 "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}"
 #end if
 #end for
 ##The if below takes care of the comma at the end of last condition within group
 #if $i != len( $conditions )
 },
 #else
 }
 #end if
 #end for
 #if len( $conditions ) > 1
 #if str( $rule_configuration.rules_selector ) == "True":
 ],
 "rule" : "${rule_configuration.rules}"
 #else
 <data format="txt" name="out_file2" />
 <data format="bam" name="out_file1" />
 </outputs>
 <tests>
 <test>
-<param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
+<param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
 <param name="bam_property_selector" value="mapQuality"/>
 <param name="bam_property_value" value=">20"/>
 <output name="out_file1" file="bamtools-test1.bam" ftype="bam"/>
 </test>
 </tests>
 <help>
 **What is does**
 **Example 1. Using a single filter**
 When filtering on a single condition there is no need to worry about filters and conditions. Just choose a filter from the **Select BAM property to filter on:** dropdown and enter a value (or click a checkbox for binary filters).
 For example, for retaining reads with mapping quality of at least 20 one would set the tool interface as shown below:
-.. image:: ${static_path}/images/single-filter.png
+.. image:: single-filter.png
 -----
 **Example 2. Using multiple filters**
 Now suppose one needs to extract reads that (1) have mapping quality of at least 20, (2) contain at least 1 mismatch, and (3) are mapping onto forward strand only.
 To do so we will use three filters as shown below (multiple filters are added to the interface by clicking on the **Add new Filter** button):
-.. image:: ${static_path}/images/multiple-filters.png
+.. image:: multiple-filters.png
 In this case (you can see that the three filters are grouped within a single Condition - **Condition 1**) the filter too use logical **AND** to perform filtering.
 In other words only reads that (1) have mapping quality of at least 20 **AND** (2) contain at least 1 mismatch **AND** are mapping onto forward strand will be returned in this example.
 -----
 **Example 3. Complex filtering with multiple conditions**
 Suppose now you would like to select **either** reads that (**1**) have (*1.1*) no mismatches and (*1.2*) are on the forward strand **OR** (**2**) reads that have (*2.1*)
 at least one mismatch and (*2.2*) are on the reverse strand. In this scenario we have to set up two conditions: (**1**) and (**2**) each with two filters: *1.1* and *1.2* as well as *2.1* and *2.2*.
 The following screenshot expalins how this can be done:
-.. image:: ${static_path}/images/complex-filters.png
+.. image:: complex-filters.png
 -----
 **Example 4. Even more complex filtering with Rules**
 In the above example we have used two conditions (Condition 1 and Condition 2). Using multiple conditions allows to combine them and a variety of ways to enable even more powerful filtering.
 For example, suppose get all reads that (**1**) do NOT map to mitochondria and either (**2**) have mapping quality over 20, or (**3**) are in properly mapped pairs. The logical rule to enable such
 filtering will look like this::
 !(1) &amp; (2 | 3)
 Here, numbers 1, 2, and 3 represent conditions. The following screenshot illustrates how to do this in Galaxy:
-.. image:: ${static_path}/images/rule.png
+.. image:: rule.png
 There are three conditions here, each with a single filter. A text entry area that can be opened by clicking on the **Would you like to set rules?** checkbox enables you to enter a rule.
 Here numbers correspond to numbers of conditions as they are shown in the interface. E.g., 1 corresponds to condition 1, 2 to condition 2 and so on... In human language this means::
 NOT condition 1 AND (condition 2 OR condition 3)
 "tag":"NM:>0",
 "isReverseStrand":"true"
 }
 ]
 }
 -----
 **More information**

Mercurial > repos > devteam > bamtools_filter

comparison bamtools-filter.xml @ 2:2098a49ddf66 draft