| Previous changeset 4:6cbfede05833 (2020-06-16) Next changeset 6:28b94cfbfdb9 (2024-10-05) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm commit 6b66cbbde16c35593fe95066ea2b91623bf35140" |
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modified:
cuff_macros.xml cuffnorm_wrapper.xml |
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| diff -r 6cbfede05833 -r 9a854107dbb2 cuff_macros.xml --- a/cuff_macros.xml Tue Jun 16 13:01:30 2020 -0400 +++ b/cuff_macros.xml Fri Jul 03 11:44:40 2020 -0400 |
| [ |
| b'@@ -1,91 +1,95 @@\n <macros>\n- <token name="@VERSION@">2.2.1</token>\n+ <token name="@VERSION@">2.2.1</token>\n+\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="2.2.1">cufflinks</requirement>\n+ <yield />\n+ </requirements>\n+ </xml>\n \n- <xml name="requirements">\n- <requirements>\n- <requirement type="package" version="2.2.1">cufflinks</requirement>\n- <yield />\n- </requirements>\n- </xml>\n+ <xml name="conditions_repeat" token_format="">\n+ <repeat name="conditions" title="Condition" min="2">\n+ <param name="name" label="Condition name" type="text">\n+ <validator type="empty_field" message="You must provide a condition name" />\n+ <validator type="expression" message="Commas are not allowed in condition names">value and "," not in value</validator>\n+ </param>\n+ <param name="samples" label="Replicates" type="data" format="@FORMAT@" multiple="true"/>\n+ </repeat>\n+ </xml>\n \n- <xml name="condition_inputs">\n- <!-- DEFAULT : use BAM/SAM files -->\n- <conditional name="in_type">\n- <param name="set_in_type" type="select" label="Input data type"\n- help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM">\n- <option value="BAM">SAM/BAM</option>\n- <option value="CXB">Cuffquant (CXB)</option>\n- <option value="CONDITION_LIST">List of single replicate conditions</option>\n- <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option>\n- </param>\n- <when value="BAM">\n- <repeat name="conditions" title="Condition" min="2">\n- <param name="name" label="Condition name" type="text"/>\n- <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/>\n- </repeat>\n- </when>\n- <when value="CXB">\n- <repeat name="conditions" title="Condition" min="2">\n- <param name="name" label="Condition name" type="text"/>\n- <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/>\n- </repeat>\n- </when>\n- <when value="CONDITION_LIST">\n- <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" />\n- </when>\n- <when value="CONDITION_REPLICATE_LIST">\n- <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" />\n- </when>\n- </conditional>\n- </xml>\n- <token name="@CONDITION_SAMPLES@">\n- #if $in_type.set_in_type in [\'BAM\', \'CXB\']\n- #for $condition in $in_type.conditions:\n- #set samples = \',\'.join( [ str( $sample ) for $sample in $condition.samples ] )\n- \'$samples\'\n- #end for\n- #elif $in_type.set_in_type == \'CONDITION_LIST\'\n- #for $sample in $in_type.conditions:\n- \'$sample\'\n- #end for\n- #elif $in_type.set_in_type == \'CONDITION_REPLICATE_LIST\'\n- #for $condition_list in $in_type.conditions:\n- #set samples = \',\'.join( [ str( $sample ) for $sample in $condition_list ] )\n- \'$samples\'\n- #end for\n- #end if\n- </token>\n- <token name="@CONDITION_LABELS@">\n- #import re\n- #if $in_type.set_in_type in [\'BAM\', \'CXB\']\n- #set labels = \'\\\'\' + \'\\\',\\\'\'.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + \'\\\'\'\n- #elif $in_type.set_in_type in [\'CONDITION_LIST\', \'CONDITION_REPLICATE_LIST\']\n- #set labels = \'\\\'\' + \'\\\',\\\'\'.join( map(lambda x: re.sub(\'[^\\w\\-_]\', \'_\', x), $in_type.conditions.keys() ) ) + \'\\\'\'\n- #end if\n- --labels'..b's\n- </token>\n- <xml name="cufflinks_gtf_inputs">\n- <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" />\n- </xml>\n- <token name="@CUFFLINKS_LINK_GTF_INPUTS@"><![CDATA[\n- ## Inputs.\n- #for $i, $input_file in enumerate($inputs):\n- ln -s \'${input_file}\' input_$i &&\n- #end for\n- ]]></token>\n- <token name="@CUFFLINKS_GTF_INPUTS@">\n- ## Inputs.\n- #for $i, $input_file in enumerate($inputs):\n- \'input_$i\'\n- #end for\n- </token>\n- <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>\n+ <xml name="condition_inputs">\n+ <!-- DEFAULT : use BAM/SAM files -->\n+ <conditional name="in_type">\n+ <param name="set_in_type" type="select" label="Input data type"\n+ help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM">\n+ <option value="BAM">SAM/BAM</option>\n+ <option value="CXB">Cuffquant (CXB)</option>\n+ <option value="CONDITION_LIST">List of single replicate conditions</option>\n+ <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option>\n+ </param>\n+ <when value="BAM">\n+ <expand macro="conditions_repeat" format="sam,bam" />\n+ </when>\n+ <when value="CXB">\n+ <expand macro="conditions_repeat" format="cxb" />\n+ </when>\n+ <when value="CONDITION_LIST">\n+ <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" />\n+ </when>\n+ <when value="CONDITION_REPLICATE_LIST">\n+ <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" />\n+ </when>\n+ </conditional>\n+ </xml>\n+ <token name="@CONDITION_SAMPLES@"><![CDATA[\n+#if $in_type.set_in_type in [\'BAM\', \'CXB\']\n+ #for $condition in $in_type.conditions:\n+ #set samples = \',\'.join([str($sample) for $sample in $condition.samples])\n+ \'$samples\'\n+ #end for\n+#elif $in_type.set_in_type == \'CONDITION_LIST\'\n+ #for $sample in $in_type.conditions:\n+ \'$sample\'\n+ #end for\n+#elif $in_type.set_in_type == \'CONDITION_REPLICATE_LIST\'\n+ #for $condition_list in $in_type.conditions:\n+ #set samples = \',\'.join([str($sample) for $sample in $condition_list])\n+ \'$samples\'\n+ #end for\n+#end if\n+ ]]></token>\n+ <token name="@CONDITION_LABELS@"><![CDATA[\n+#import re\n+#if $in_type.set_in_type in [\'BAM\', \'CXB\']\n+ #set labels = "\',\'".join([str($condition.name) for $condition in $in_type.conditions])\n+#elif $in_type.set_in_type in [\'CONDITION_LIST\', \'CONDITION_REPLICATE_LIST\']\n+ #set labels = "\',\'".join([str($condition).replace(\',\', \'_\') for $condition in $in_type.conditions.keys()])\n+#end if\n+--labels \'$labels\'\n+ ]]></token>\n+ <xml name="cufflinks_gtf_inputs">\n+ <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" />\n+ </xml>\n+ <token name="@CUFFLINKS_LINK_GTF_INPUTS@"><![CDATA[\n+## Inputs.\n+#for $i, $input_file in enumerate($inputs):\n+ ln -s \'${input_file}\' input_$i &&\n+#end for\n+ ]]></token>\n+ <token name="@CUFFLINKS_GTF_INPUTS@"><![CDATA[\n+## Inputs.\n+#for $i, $input_file in enumerate($inputs):\n+ \'input_$i\'\n+#end for\n+ ]]></token>\n+ <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>\n \n- <xml name="citations">\n- <citations>\n- <citation type="doi">10.1038/nbt.1621</citation>\n- <yield/>\n- </citations>\n- </xml>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1038/nbt.1621</citation>\n+ <yield/>\n+ </citations>\n+ </xml>\n \n </macros>\n' |
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| diff -r 6cbfede05833 -r 9a854107dbb2 cuffnorm_wrapper.xml --- a/cuffnorm_wrapper.xml Tue Jun 16 13:01:30 2020 -0400 +++ b/cuffnorm_wrapper.xml Fri Jul 03 11:44:40 2020 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="cuffnorm" name="Cuffnorm" version="@VERSION@.2"> +<tool id="cuffnorm" name="Cuffnorm" version="@VERSION@.3"> <description>Create normalized expression levels</description> <macros> <import>cuff_macros.xml</import> @@ -210,7 +210,7 @@ **Input format** -Cuffdiff takes Cufflinks or Cuffcompare GTF files as input along with two SAM files containing the fragment alignments for two or more samples. +Cuffnorm takes Cufflinks or Cuffcompare GTF files as input along with two SAM files containing the fragment alignments for two or more samples. ------ @@ -223,15 +223,9 @@ ------- -**Settings** - -All of the options have a default value. You can change any of them. Most of the options in Cuffdiff have been implemented here. +**Parameter list** ------- - -**Cuffdiff parameter list** - -This is a list of implemented Cuffdiff options:: +This is a list of implemented Cuffnorm options:: --library-norm-method Library Normalization method : Geometric (default), classic-fpkm, quartile --library-type ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags |