diff --git a/tools/picard/rgPicardASMetrics.xml b/tools/picard/rgPicardASMetrics.xml index 9ae2cbbe83d..6f3d6b1ae18 100644 --- a/tools/picard/rgPicardASMetrics.xml +++ b/tools/picard/rgPicardASMetrics.xml @@ -183,24 +183,6 @@ This seems an awful strategy but unfortunately may be needed to run an analysis Picard and Samtools go together. They are external to and completely independent of Galaxy. We acknowledge that all credit for their methods and contribution are due to them. -Here, you can apply Picard tools through Galaxy which you may find much easier than through the native Picard command line interface. - - - ------ - -.. class:: infomark - -**Copyright** - -This Galaxy tool is a component of the rgenetics toolkit. - -Written by and copyright Ross Lazarus, ross.lazarus at gmail etc, September 2010 - -All rgenetics artefacts are available licensed under the LGPL_ -Other dependencies are licensed at the author's discretion - please see each individual package for details - - .. _LGPL: http://www.gnu.org/copyleft/lesser.html diff --git a/tools/picard/rgPicardFixMate.xml b/tools/picard/rgPicardFixMate.xml index a8d24fed8a6..538e842a5b0 100644 --- a/tools/picard/rgPicardFixMate.xml +++ b/tools/picard/rgPicardFixMate.xml @@ -101,7 +101,7 @@ or by providing comments through the report form that appears automatically if a tool fails unexpectedly when you run it in Galaxy. All the Picard tools are freely available and are documented -at http://picard.sourceforge.net/command-line-overview.shtml#CollectAlignmentSummaryMetrics +at http://picard.sourceforge.net/command-line-overview.shtml Written by and copyright Ross Lazarus, ross.lazarus at gmail etc, September 2010 Code cleaned up and the ugliest hacks repaired by Raphael Lullis. @@ -109,18 +109,6 @@ Kelly Vincent wrote the first version of picard_wrapper.py that now incorporates It takes a village of programmers to wrap a picard tool ------ - -.. class:: infomark - -**Copyright** - -This Galaxy tool is a component of the rgenetics toolkit. - -All rgenetics artefacts are available licensed under the LGPL_ -Other dependencies are licensed at the author's discretion - please see each individual package for details - - .. _LGPL: http://www.gnu.org/copyleft/lesser.html diff --git a/tools/picard/rgPicardGCBiasMetrics.xml b/tools/picard/rgPicardGCBiasMetrics.xml index 1eaa1d90a9b..89dfb3039ca 100644 --- a/tools/picard/rgPicardGCBiasMetrics.xml +++ b/tools/picard/rgPicardGCBiasMetrics.xml @@ -162,22 +162,5 @@ Picard and Samtools go together. They are external to and completely independent of Galaxy. We acknowledge that all credit for their methods and contribution are due to them. -Here, you can apply Picard tools through Galaxy which might be easier than through the native Picard command line interface. - - ------ - -.. class:: infomark - -**Copyright** - -This Galaxy tool is a component of the rgenetics toolkit. - -Written by and copyright Ross Lazarus, ross.lazarus at gmail etc, September 2010 -All rgenetics artefacts are available licensed under the LGPL_ -Other dependencies are licensed at the author's discretion - please see each individual package for details - - .. _LGPL: http://www.gnu.org/copyleft/lesser.html - diff --git a/tools/picard/rgPicardHsMetrics.xml b/tools/picard/rgPicardHsMetrics.xml index 7bb2b563603..09b1324e36e 100644 --- a/tools/picard/rgPicardHsMetrics.xml +++ b/tools/picard/rgPicardHsMetrics.xml @@ -1,5 +1,5 @@ - For (eg exome) targetted data + For (eg exome) targeted data picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --datatype "$input_file.ext" @@ -139,19 +139,6 @@ This Galaxy tool uses part of Picard to report measures of hybridization selecti aligned short read sequence data. Sequence data must be chosen from the sam/bam format files in your current history. Target and bait files must be selected from the UCSC BED format in your current history. ------ - -.. class:: infomark - -**Copyright** - -This is part of the rgenetics toolkit. - -Written by Ross Lazarus 2010 -All rgenetics artefacts are available licensed under the LGPL_ -Other dependencies are licensed at the author's discretion - please see each individual package for details - - .. _LGPL: http://www.gnu.org/copyleft/lesser.html diff --git a/tools/picard/rgPicardInsertSize.xml b/tools/picard/rgPicardInsertSize.xml index 49647a6df4d..3eaf28bc1da 100644 --- a/tools/picard/rgPicardInsertSize.xml +++ b/tools/picard/rgPicardInsertSize.xml @@ -78,23 +78,8 @@ or by providing comments through the report form that appears automatically if a tool fails unexpectedly when you run it in Galaxy. All the Picard tools are freely available and are documented -at http://picard.sourceforge.net/command-line-overview.shtml#CollectInsertSizeMetrics +at http://picard.sourceforge.net/command-line-overview.shtml -Here, you can apply Picard tools through Galaxy which might be easier than through the native Picard command line interface. - ------ - -.. class:: infomark - -**Copyright** - -This Galaxy tool is a component of the rgenetics toolkit. - -Written by and copyright Ross Lazarus, ross.lazarus at gmail etc, September 2010 -Code cleaned up and the ugliest hacks repaired by Raphael Lullis - -All rgenetics artifacts are available licensed under the LGPL -Other dependencies are licensed at the author's discretion - please see each individual package for details diff --git a/tools/picard/rgPicardLibComplexity.xml b/tools/picard/rgPicardLibComplexity.xml index ed12007b258..59f29b73d4d 100644 --- a/tools/picard/rgPicardLibComplexity.xml +++ b/tools/picard/rgPicardLibComplexity.xml @@ -121,22 +121,6 @@ if a tool fails unexpectedly when you run it in Galaxy. All the Picard tools are freely available and are documented at http://picard.sourceforge.net/command-line-overview.shtml#CollectInsertSizeMetrics ------ - -.. class:: infomark - -**Copyright** - -This Galaxy tool is a component of the rgenetics toolkit. - -Written by and copyright Ross Lazarus, ross.lazarus at gmail etc, September 2010 -Code cleaned up and the ugliest hacks repaired by Raphael Lullis - -All rgenetics artefacts are available licensed under the LGPL_ -Other dependencies are licensed at the author's discretion - please see each individual package for details - - .. _LGPL: http://www.gnu.org/copyleft/lesser.html - diff --git a/tools/picard/rgPicardMarkDups.xml b/tools/picard/rgPicardMarkDups.xml index 68eb07f6ba1..21feba086f0 100644 --- a/tools/picard/rgPicardMarkDups.xml +++ b/tools/picard/rgPicardMarkDups.xml @@ -120,24 +120,6 @@ if a tool fails unexpectedly when you run it in Galaxy. All the Picard tools are freely available and are documented at http://picard.sourceforge.net/command-line-overview.shtml#CollectInsertSizeMetrics -Here, you can apply Picard tools through Galaxy which might be easier than through the native Picard command line interface. - ------ - -.. class:: infomark - -**Copyright** - -This Galaxy tool is a component of the rgenetics toolkit. - -Written by and copyright Ross Lazarus, ross.lazarus at gmail etc, September 2010 -Code cleaned up and the ugliest hacks repaired by Raphael Lullis - -All rgenetics artifacts are available licensed under the LGPL_ -Other dependencies are licensed at the author's discretion - please see each individual package for details - -.. _LGPL: http://www.gnu.org/copyleft/lesser.html -