| Previous changeset 1:d64c7e752f4d (2015-03-09) Next changeset 3:29ba2103739c (2017-01-13) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7 |
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modified:
bamtools-filter.xml tool_dependencies.xml |
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| diff -r d64c7e752f4d -r 2098a49ddf66 bamtools-filter.xml --- a/bamtools-filter.xml Mon Mar 09 14:07:23 2015 -0400 +++ b/bamtools-filter.xml Wed Nov 11 12:33:46 2015 -0500 |
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| b'@@ -1,32 +1,27 @@\n-<tool id="bamFilter" name="Filter" version="0.0.1">\r\n+<tool id="bamFilter" name="Filter" version="0.0.2">\r\n <description>BAM datasets on a variety of attributes</description>\r\n <requirements>\r\n <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement>\r\n </requirements>\r\n <command>\r\n+ cat $script_file > $out_file2;\r\n \r\n- cat $script_file > $out_file2;\r\n- \r\n #for $bam_count, $input_bam in enumerate( $input_bams ):\r\n- ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &&\r\n- ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&\r\n+ ln -s "${input_bam}" "localbam_${bam_count}.bam" &&\r\n+ ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&\r\n #end for\r\n- \r\n+\r\n bamtools\r\n filter\r\n -script $script_file\r\n- \r\n+\r\n #for $bam_count, $input_bam in enumerate( $input_bams ):\r\n -in "localbam_${bam_count}.bam"\r\n #end for\r\n -out $out_file1\r\n- \r\n </command>\r\n-\r\n <inputs>\r\n- <repeat name="input_bams" title="BAM dataset(s) to filter" min="1">\r\n- <param name="input_bam" type="data" format="bam" label="BAM dataset" />\r\n- </repeat>\r\n+ <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/>\r\n <repeat name="conditions" title="Condition" min="1">\r\n <repeat name="filters" title="Filter" min="1">\r\n <conditional name="bam_property">\r\n@@ -59,10 +54,10 @@\n <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"/>\r\n </when>\r\n <when value="cigar">\r\n- <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"/>\r\n+ <param name="bam_property_value" type="text" value="101M" label="Filter on this CIGAR string" help="Default (101M) is for 101 continuously matched bases"/>\r\n </when>\r\n <when value="insertSize">\r\n- <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"">\r\n+ <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"">\r\n <sanitizer invalid_char="">\r\n <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid>\r\n </sanitizer>\r\n@@ -164,7 +159,7 @@\n <conditional name="rule_configuration">\r\n <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." />\r\n <when value="true">\r\n- <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." >\r\n+ <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." >\r\n <sanitizer invalid_char="">\r\n <valid initial="string.printable"/>\r\n </sanitizer>\r\n@@ -185,20 +180,20 @@\n #for $i, $c in enumerate( $conditions, start=1 )\r\n { "id": "$i",\r\n #for $j, $s in enumerate( $c.filters, start=1 )\r\n- ##The if below takes care of the comma at the end of last condition within group \r\n+ ##The if below takes care of the co'..b'takes care of the comma at the end of last condition within group \r\n+ ##The if below takes care of the comma at the end of last condition within group\r\n #if $i != len( $conditions )\r\n },\r\n #else\r\n }\r\n- #end if \r\n- #end for \r\n+ #end if\r\n+ #end for\r\n #if len( $conditions ) > 1\r\n #if str( $rule_configuration.rules_selector ) == "True":\r\n ],\r\n@@ -217,10 +212,10 @@\n </outputs>\r\n <tests>\r\n <test>\r\n- <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>\r\n+ <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>\r\n <param name="bam_property_selector" value="mapQuality"/>\r\n <param name="bam_property_value" value=">20"/>\r\n- <output name="out_file1" file="bamtools-test1.bam" ftype="bam"/> \r\n+ <output name="out_file1" file="bamtools-test1.bam" ftype="bam"/>\r\n </test>\r\n </tests>\r\n <help>\r\n@@ -249,7 +244,7 @@\n 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).\r\n For example, for retaining reads with mapping quality of at least 20 one would set the tool interface as shown below:\r\n \r\n-.. image:: ${static_path}/images/single-filter.png\r\n+.. image:: single-filter.png\r\n \r\n -----\r\n \r\n@@ -258,7 +253,7 @@\n 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.\r\n 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):\r\n \r\n-.. image:: ${static_path}/images/multiple-filters.png\r\n+.. image:: multiple-filters.png\r\n \r\n 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.\r\n 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.\r\n@@ -267,11 +262,11 @@\n \r\n **Example 3. Complex filtering with multiple conditions**\r\n \r\n-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*) \r\n-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*. \r\n+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*)\r\n+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*.\r\n The following screenshot expalins how this can be done:\r\n \r\n-.. image:: ${static_path}/images/complex-filters.png\r\n+.. image:: complex-filters.png\r\n \r\n -----\r\n \r\n@@ -282,10 +277,10 @@\n filtering will look like this::\r\n \r\n !(1) & (2 | 3)\r\n- \r\n+\r\n Here, numbers 1, 2, and 3 represent conditions. The following screenshot illustrates how to do this in Galaxy:\r\n \r\n-.. image:: ${static_path}/images/rule.png\r\n+.. image:: rule.png\r\n \r\n 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.\r\n 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::\r\n@@ -312,8 +307,7 @@\n }\r\n ]\r\n }\r\n- \r\n- \r\n+\r\n \r\n -----\r\n \r\n' |
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| diff -r d64c7e752f4d -r 2098a49ddf66 tool_dependencies.xml --- a/tool_dependencies.xml Mon Mar 09 14:07:23 2015 -0400 +++ b/tool_dependencies.xml Wed Nov 11 12:33:46 2015 -0500 |
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| @@ -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> |