| Previous changeset 8:1322b73ffe44 (2017-02-07) Next changeset 10:f648e5180e40 (2020-06-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5 |
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modified:
cuff_macros.xml cuffcompare_wrapper.py cuffcompare_wrapper.xml |
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removed:
tool_dependencies.xml |
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| diff -r 1322b73ffe44 -r e66b9b5b8580 cuff_macros.xml --- a/cuff_macros.xml Tue Feb 07 18:38:41 2017 -0500 +++ b/cuff_macros.xml Sun Feb 19 12:12:05 2017 -0500 |
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| @@ -8,14 +8,6 @@ </requirements> </xml> - <xml name="stdio"> - <stdio> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <regex match="Error" /> - <regex match="Exception" /> - </stdio> - </xml> <xml name="condition_inputs"> <!-- DEFAULT : use BAM/SAM files --> <conditional name="in_type"> |
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| diff -r 1322b73ffe44 -r e66b9b5b8580 cuffcompare_wrapper.py --- a/cuffcompare_wrapper.py Tue Feb 07 18:38:41 2017 -0500 +++ b/cuffcompare_wrapper.py Sun Feb 19 12:12:05 2017 -0500 |
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| @@ -38,23 +38,6 @@ (options, args) = parser.parse_args() - # output version # of tool - try: - with tempfile.NamedTemporaryFile() as tmp_stdout: - returncode = subprocess.call(args='cuffcompare 2>&1', stdout=tmp_stdout, shell=True) - stdout = None - with open(tmp_stdout.name) as tmp_stdout2: - for line in tmp_stdout2: - if line.lower().find('cuffcompare v') >= 0: - stdout = line.strip() - break - if stdout: - sys.stdout.write('%s\n' % stdout) - else: - raise Exception - except: - sys.stdout.write('Could not determine Cuffcompare version\n') - # Set/link to sequence file. if options.use_seq_data: if options.ref_file: |
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| diff -r 1322b73ffe44 -r e66b9b5b8580 cuffcompare_wrapper.xml --- a/cuffcompare_wrapper.xml Tue Feb 07 18:38:41 2017 -0500 +++ b/cuffcompare_wrapper.xml Sun Feb 19 12:12:05 2017 -0500 |
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| b'@@ -1,12 +1,11 @@\n-<tool id="cuffcompare" name="Cuffcompare" version="2.2.1.0">\n+<tool id="cuffcompare" name="Cuffcompare" version="@VERSION@.1">\n <description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description>\n <macros>\n <import>cuff_macros.xml</import>\n </macros>\n <expand macro="requirements" />\n- <expand macro="stdio" />\n <version_command>cuffcompare 2>&1 | head -n 1</version_command>\n- <command>\n+ <command detect_errors="aggressive"><![CDATA[\n python \'$__tool_directory__/cuffcompare_wrapper.py\'\n ## Use annotation reference?\n #if $annotation.use_ref_annotation == "Yes":\n@@ -19,7 +18,7 @@\n #end if\n \n #end if\n- \n+\n ## Use sequence data?\n #if $seq_data.use_seq_data == "Yes":\n -s\n@@ -29,7 +28,7 @@\n --index \'${seq_data.seq_source.index.fields.path}\'\n #end if\n #end if\n- \n+\n $discard_single_exon\n \n -e $max_dist_exon\n@@ -37,13 +36,13 @@\n \n #if $discard_intron_redundant_transfrags:\n -F\n- #end if \n+ #end if\n \n ## Outputs.\n --combined-transcripts \'${transcripts_combined}\'\n \n @CUFFLINKS_GTF_INPUTS@\n- </command>\n+ ]]></command>\n <inputs>\n <expand macro="cufflinks_gtf_inputs" />\n <conditional name="annotation">\n@@ -60,7 +59,7 @@\n </when>\n </conditional>\n <conditional name="seq_data">\n- <param name="use_seq_data" type="select" label="Use Sequence Data" \n+ <param name="use_seq_data" type="select" label="Use Sequence Data"\n help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff.">\n <option value="Yes">Yes</option>\n <option value="No">No</option>\n@@ -91,29 +90,29 @@\n <option value="-M">Discard single-exon transfrags and reference transcripts</option>\n <option value="-N">Discard single-exon reference transcripts</option>\n </param>\n- <param type="integer" name="max_dist_exon" value="100" label="Max. Distance for assessing exon accuracy" \n+ <param type="integer" name="max_dist_exon" value="100" label="Max. Distance for assessing exon accuracy"\n help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100" />\n- <param type="integer" name="max_dist_group" value="100" label="Max.Distance for transcript grouping" \n+ <param type="integer" name="max_dist_group" value="100" label="Max.Distance for transcript grouping"\n help="max. distance (range) for grouping transcript start sites. Default: 100" />\n- <param type="boolean" name="discard_intron_redundant_transfrags" label="discard intron-redundant transfrags sharing 5\'" \n+ <param type="boolean" name="discard_intron_redundant_transfrags" label="discard intron-redundant transfrags sharing 5\'"\n help="Discard intron-redundant transfrags if they share the 5\' end (if they differ only at the 3\' end)" />\n </inputs>\n \n <outputs>\n- <data format="txt" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy" \n+ <data format="txt" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy"\n from_work_dir="cc_output.stats" />\n <data format="tabular" name="input1_tmap" label="${tool.name} on ${on_string}: data ${inputs[0].hid} tmap file"\n from_work_dir="cc_output.input1.tmap" />\n- <data format="tabular" name="input1_refmap" \n- label="${tool.name} on ${on_string}: data ${inputs[0].hid} refmap file" \n+ <data '..b'">\n <filter>@HAS_MULTIPLE_INPUTS@</filter>\n </data>\n- <data format="tabular" name="input2_refmap" \n- label="${tool.name} on ${on_string}: data ${inputs[1].hid} refmap file" \n+ <data format="tabular" name="input2_refmap"\n+ label="${tool.name} on ${on_string}: data ${inputs[1].hid} refmap file"\n from_work_dir="cc_output.input2.refmap">\n <filter>annotation[\'use_ref_annotation\'] == \'Yes\' and @HAS_MULTIPLE_INPUTS@</filter>\n </data>\n@@ -124,7 +123,7 @@\n </outputs>\n \n <tests>\n- <!-- \n+ <!--\n cuffcompare -r cuffcompare_in3.gtf -R cuffcompare_in1.gtf cuffcompare_in2.gtf\n -->\n <test>\n@@ -173,7 +172,7 @@\n \n Cuffcompare takes Cufflinks\' GTF output as input, and optionally can take a "reference" annotation (such as from Ensembl_)\n \n-.. _Ensembl: http://www.ensembl.org \n+.. _Ensembl: http://www.ensembl.org\n \n ------\n \n@@ -187,7 +186,7 @@\n \n Transcripts Combined File:\n \n-Cuffcompare reports a GTF file containing the "union" of all transfrags in each sample. If a transfrag is present in both samples, it is thus reported once in the combined gtf. \n+Cuffcompare reports a GTF file containing the "union" of all transfrags in each sample. If a transfrag is present in both samples, it is thus reported once in the combined gtf.\n \n Transcripts Tracking File:\n \n@@ -209,7 +208,7 @@\n 3 Reference gene id Tcea The gene_name attribute of the reference GTF record for this transcript, or \'-\' if no reference transcript overlaps this Cufflinks transcript\n 4 Reference transcript id uc007afj.1 The transcript_id attribute of the reference GTF record for this transcript, or \'-\' if no reference transcript overlaps this Cufflinks transcript\n 5 Class code c The type of match between the Cufflinks transcripts in column 6 and the reference transcript. See class codes\n- \n+\n Each of the columns after the fifth have the following format:\n qJ:gene_id|transcript_id|FMI|FPKM|conf_lo|conf_hi\n \n@@ -222,18 +221,18 @@\n Priority Code Description\n ---------------------------------\n 1 = Match\n- 2 c Contained \n- 3 j New isoform \n- 4 e A single exon transcript overlapping a reference exon and at least 10 bp of a reference intron, indicating a possible pre-mRNA fragment. \n+ 2 c Contained\n+ 3 j New isoform\n+ 4 e A single exon transcript overlapping a reference exon and at least 10 bp of a reference intron, indicating a possible pre-mRNA fragment.\n 5 i A single exon transcript falling entirely with a reference intron\n 6 o Generic exonic overlap with a reference transcript\n- 7 p Possible polymerase run-on fragment \n- 8 r Repeat. Currently determined by looking at the soft-masked reference sequence and applied to transcripts where at least 50% of the bases are lower case \n+ 7 p Possible polymerase run-on fragment\n+ 8 r Repeat. Currently determined by looking at the soft-masked reference sequence and applied to transcripts where at least 50% of the bases are lower case\n 9 u Unknown, intergenic transcript\n 10 x Exonic overlap with reference on the opposite strand\n 11 s An intron of the transfrag overlaps a reference intron on the opposite strand (likely due to read mapping errors)\n 12 . (.tracking file only, indicates multiple classifications)\n- \n+\n -------\n \n **Settings**\n' |
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| diff -r 1322b73ffe44 -r e66b9b5b8580 tool_dependencies.xml --- a/tool_dependencies.xml Tue Feb 07 18:38:41 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="cufflinks" version="2.2.1"> - <repository changeset_revision="899067a260d1" name="package_cufflinks_2_2_1" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |