| Previous changeset 3:29ba2103739c (2017-01-13) Next changeset 5:bd735cae4ce6 (2017-05-25) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01 |
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modified:
bamtools-filter.xml |
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removed:
tool_dependencies.xml |
| b |
| diff -r 29ba2103739c -r 3213c223678c bamtools-filter.xml --- a/bamtools-filter.xml Fri Jan 13 11:02:24 2017 -0500 +++ b/bamtools-filter.xml Wed Jan 18 11:47:29 2017 -0500 |
| [ |
| b'@@ -1,215 +1,212 @@\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- #for $bam_count, $input_bam in enumerate( $input_bams ):\r\n- ln -s "${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- bamtools\r\n- filter\r\n- -script $script_file\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- </command>\r\n- <inputs>\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- <param name="bam_property_selector" type="select" label="Select BAM property to filter on">\r\n- <option value="alignmentFlag"/>\r\n- <option value="cigar"/>\r\n- <option value="insertSize"/>\r\n- <option value="isDuplicate"/>\r\n- <option value="isFailedQC"/>\r\n- <option value="isFirstMate"/>\r\n- <option value="isMapped"/>\r\n- <option value="isMateMapped"/>\r\n- <option value="isMateReverseStrand"/>\r\n- <option value="isPaired"/>\r\n- <option value="isPrimaryAlignment"/>\r\n- <option value="isProperPair"/>\r\n- <option value="isReverseStrand"/>\r\n- <option value="isSecondMate"/>\r\n- <option selected="True" value="mapQuality"/>\r\n- <option value="matePosition"/>\r\n- <option value="mateReference"/>\r\n- <option value="name"/>\r\n- <option value="position"/>\r\n- <option value="queryBases"/>\r\n- <option value="reference"/>\r\n- <option value="tag"/>\r\n- </param>\r\n- <!-- would be fanstastic to have AND and OR constructs in when statements -->\r\n- <when value="alignmentFlag">\r\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" 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" value=">=250" label="Filter on insert size" help="You can use >, <, =, and ! (not) in your expression. E.g., to select pairs with insert 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="!="/><add value="-"/></valid>\r\n- </sanitizer>\r\n- </param>\r\n- </when>\r\n- <when value="isDuplicate">\r\n- <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads makwed as duplicates" help="Checked = Read IS Duplicate, Empty = Read is NOT Duplicate" />\r\n- </when>\r\n- <when value="isFailedQC">\r\n- <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads failing QC" help="Checked = Failed QC, Empty = Passed QC"/>\r\n- </when>\r\n- <when value="isFirstMate">\r\n- <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select first mate in a read pair" help="Checked = is first mate, Empty = is NOT first mate"/>\r\n- '..b' </sanitizer>\r\n+ </param>\r\n+ </when>\r\n+ </conditional>\r\n+ </repeat>\r\n+ </repeat>\r\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="false"/>\r\n+ <when value="true">\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+ </param>\r\n+ </when>\r\n </conditional>\r\n- </repeat>\r\n- </repeat>\r\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" 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- </param>\r\n- </when>\r\n- </conditional>\r\n- </inputs>\r\n-\r\n- <configfiles>\r\n- <configfile name="script_file">\r\n- ##Sets up a json configfile for bamtools filter\r\n- ##If there is more than one condition prints brackets and "filters:"\r\n- #if len( $conditions ) > 1\r\n- {\r\n- "filters":\r\n- [\r\n- #end if\r\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- #if $j != len( $c.filters)\r\n- "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}",\r\n- #else\r\n- "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}"\r\n- #end if\r\n- #end for\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- #if len( $conditions ) > 1\r\n- #if str( $rule_configuration.rules_selector ) == "True":\r\n- ],\r\n- "rule" : "${rule_configuration.rules}"\r\n- #else\r\n- ]\r\n- #end if\r\n- }\r\n- #end if\r\n- </configfile>\r\n- </configfiles>\r\n-\r\n- <outputs>\r\n- <data format="txt" name="out_file2" />\r\n- <data format="bam" name="out_file1" />\r\n- </outputs>\r\n+ </inputs>\r\n+ <outputs>\r\n+ <data format="txt" name="out_file2" />\r\n+ <data format="bam" name="out_file1" />\r\n+ </outputs>\r\n <tests>\r\n <test>\r\n <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>\r\n@@ -218,7 +215,7 @@\n <output name="out_file1" file="bamtools-test1.bam" ftype="bam"/>\r\n </test>\r\n </tests>\r\n-<help>\r\n+ <help>\r\n **What is does**\r\n \r\n BAMTools filter is a very powerful utility to perform complex filtering of BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).\r\n@@ -318,8 +315,8 @@\n Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki\r\n \r\n \r\n-</help>\r\n- <citations>\r\n- <citation type="doi">10.1093/bioinformatics/btr174</citation>\r\n- </citations>\r\n+ </help>\r\n+ <citations>\r\n+ <citation type="doi">10.1093/bioinformatics/btr174</citation>\r\n+ </citations>\r\n </tool>\r\n' |
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| diff -r 29ba2103739c -r 3213c223678c tool_dependencies.xml --- a/tool_dependencies.xml Fri Jan 13 11:02:24 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="bamtools" version="2.3.0_2d7685d2ae"> - <repository changeset_revision="7d6da4982f19" name="package_bamtools_2_3_0_2d7685d2ae" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |