Mercurial > repos > devteam > bamtools_filter
changeset 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 |
| files | bamtools-filter.xml tool_dependencies.xml |
| diffstat | 2 files changed, 25 insertions(+), 31 deletions(-) [+] |
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--- a/bamtools-filter.xml Mon Mar 09 14:07:23 2015 -0400 +++ b/bamtools-filter.xml Wed Nov 11 12:33:46 2015 -0500 @@ -1,32 +1,27 @@ -<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; - cat $script_file > $out_file2; - #for $bam_count, $input_bam in enumerate( $input_bams ): - ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" && - ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" && + ln -s "${input_bam}" "localbam_${bam_count}.bam" && + ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" && #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_bam" type="data" format="bam" label="BAM dataset" /> - </repeat> + <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/> <repeat name="conditions" title="Condition" min="1"> <repeat name="filters" title="Filter" min="1"> <conditional name="bam_property"> @@ -59,10 +54,10 @@ <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 >, <, =, and ! (not) in your expression. E.g., to select pairs with inster size above 250 nt use ">=250""> + <param name="bam_property_value" type="text" value=">=250" label="Filter on inster size" help="You can use >, <, =, and ! (not) in your expression. E.g., to select pairs with inster size above 250 nt use ">=250""> <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> </sanitizer> @@ -164,7 +159,7 @@ <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> @@ -185,20 +180,20 @@ #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 + ##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 + ##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 + #end if + #end for #if len( $conditions ) > 1 #if str( $rule_configuration.rules_selector ) == "True": ], @@ -217,10 +212,10 @@ </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"/> + <output name="out_file1" file="bamtools-test1.bam" ftype="bam"/> </test> </tests> <help> @@ -249,7 +244,7 @@ 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 ----- @@ -258,7 +253,7 @@ 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. @@ -267,11 +262,11 @@ **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*. +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 ----- @@ -282,10 +277,10 @@ filtering will look like this:: !(1) & (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:: @@ -312,8 +307,7 @@ } ] } - - + -----
--- a/tool_dependencies.xml Mon Mar 09 14:07:23 2015 -0400 +++ b/tool_dependencies.xml Wed Nov 11 12:33:46 2015 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="bamtools" version="2.3.0_2d7685d2ae"> - <repository changeset_revision="4e49af060657" name="package_bamtools_2_3_0_2d7685d2ae" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="7d6da4982f19" name="package_bamtools_2_3_0_2d7685d2ae" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>