| Previous changeset 20:2a17c789e0a5 (2018-06-19) Next changeset 22:f6ced08779c4 (2019-03-29) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 78c3dea7dcd0c854fe7e6dc1d2b2349956167661 |
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modified:
picard_EstimateLibraryComplexity.xml picard_MarkDuplicates.xml picard_MarkDuplicatesWithMateCigar.xml picard_macros.xml |
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| diff -r 2a17c789e0a5 -r 6f9c0884a3e7 picard_EstimateLibraryComplexity.xml --- a/picard_EstimateLibraryComplexity.xml Tue Jun 19 11:28:49 2018 -0400 +++ b/picard_EstimateLibraryComplexity.xml Tue Oct 16 11:49:10 2018 -0400 |
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| @@ -18,8 +18,7 @@ MAX_DIFF_RATE="${max_diff_rate}" MIN_MEAN_QUALITY="${min_mean_quality}" MAX_GROUP_RATIO="${max_group_ratio}" - #import pipes - READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" } + READ_NAME_REGEX='${ str( $read_name_regex ) }' OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}" VALIDATION_STRINGENCY="${validation_stringency}" @@ -36,10 +35,7 @@ <param name="max_group_ratio" type="integer" value="500" label="Do not process self-similar groups that are this many times over the mean expected group size" help="MAX_GROUP_RATIO; I.e. if the input contains 10m read pairs and MIN_IDENTICAL_BASES is set to 5, then the mean expected group size would be approximately 10 reads; default-500"/> <param name="read_name_regex" type="text" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*." label="Regular expression that can be used to parse read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."> - <sanitizer> - <valid initial="string.printable"> - </valid> - </sanitizer> + <expand macro="sanitize_query" /> </param> <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/> |
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| diff -r 2a17c789e0a5 -r 6f9c0884a3e7 picard_MarkDuplicates.xml --- a/picard_MarkDuplicates.xml Tue Jun 19 11:28:49 2018 -0400 +++ b/picard_MarkDuplicates.xml Tue Oct 16 11:49:10 2018 -0400 |
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| @@ -24,9 +24,8 @@ DUPLICATE_SCORING_STRATEGY='${duplicate_scoring_strategy}' - #import pipes #if $read_name_regex: - READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) } + READ_NAME_REGEX='${ str( $read_name_regex ) }' #end if OPTICAL_DUPLICATE_PIXEL_DISTANCE='${optical_duplicate_pixel_distance}' @@ -55,11 +54,7 @@ </param> <param name="read_name_regex" type="text" value="" label="Regular expression that can be used in unusual situations to parse non-standard read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default='' (uses : separation)"> - - <sanitizer> - <valid initial="string.printable"> - </valid> - </sanitizer> + <expand macro="sanitize_query" /> </param> <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/> |
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| diff -r 2a17c789e0a5 -r 6f9c0884a3e7 picard_MarkDuplicatesWithMateCigar.xml --- a/picard_MarkDuplicatesWithMateCigar.xml Tue Jun 19 11:28:49 2018 -0400 +++ b/picard_MarkDuplicatesWithMateCigar.xml Tue Oct 16 11:49:10 2018 -0400 |
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| @@ -26,8 +26,7 @@ DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}" - #import pipes - READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" } + READ_NAME_REGEX='${ str( $read_name_regex ) }' OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}" @@ -54,10 +53,7 @@ <param name="read_name_regex" type="text" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*." label="Regular expression that can be used to parse read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."> - <sanitizer> - <valid initial="string.printable"> - </valid> - </sanitizer> + <expand macro="sanitize_query" /> </param> <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/> |
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| diff -r 2a17c789e0a5 -r 6f9c0884a3e7 picard_macros.xml --- a/picard_macros.xml Tue Jun 19 11:28:49 2018 -0400 +++ b/picard_macros.xml Tue Oct 16 11:49:10 2018 -0400 |
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| @@ -9,6 +9,17 @@ </param> </xml> + <xml name="sanitize_query"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'" /> + </valid> + <mapping initial="none"> + <add source="'" target="'"'"'" /> + </mapping> + </sanitizer> + </xml> + <token name="@TOOL_VERSION@">2.18.2</token> <xml name="requirements"> |