Mercurial > repos > devteam > cuffcompare
comparison cuffcompare_wrapper.xml @ 3:5aac9b9d6f2a draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
author | devteam |
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date | Sun, 19 Feb 2017 12:11:14 -0500 |
parents | a5674ddf2ad7 |
children | 806c27c97df7 |
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2:a5674ddf2ad7 | 3:5aac9b9d6f2a |
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1 <tool id="cuffcompare" name="Cuffcompare" version="2.2.1.0"> | 1 <tool id="cuffcompare" name="Cuffcompare" version="@VERSION@.1"> |
2 <description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description> | 2 <description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description> |
3 <macros> | 3 <macros> |
4 <import>cuff_macros.xml</import> | 4 <import>cuff_macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
7 <expand macro="stdio" /> | |
8 <version_command>cuffcompare 2>&1 | head -n 1</version_command> | 7 <version_command>cuffcompare 2>&1 | head -n 1</version_command> |
9 <command> | 8 <command detect_errors="aggressive"><![CDATA[ |
10 python '$__tool_directory__/cuffcompare_wrapper.py' | 9 python '$__tool_directory__/cuffcompare_wrapper.py' |
11 ## Use annotation reference? | 10 ## Use annotation reference? |
12 #if $annotation.use_ref_annotation == "Yes": | 11 #if $annotation.use_ref_annotation == "Yes": |
13 -r '$annotation.reference_annotation' | 12 -r '$annotation.reference_annotation' |
14 #if $annotation.ignore_nonoverlapping_reference: | 13 #if $annotation.ignore_nonoverlapping_reference: |
17 #if $annotation.ignore_nonoverlapping_transfrags: | 16 #if $annotation.ignore_nonoverlapping_transfrags: |
18 -Q | 17 -Q |
19 #end if | 18 #end if |
20 | 19 |
21 #end if | 20 #end if |
22 | 21 |
23 ## Use sequence data? | 22 ## Use sequence data? |
24 #if $seq_data.use_seq_data == "Yes": | 23 #if $seq_data.use_seq_data == "Yes": |
25 -s | 24 -s |
26 #if $seq_data.seq_source.index_source == "history": | 25 #if $seq_data.seq_source.index_source == "history": |
27 --ref_file '$seq_data.seq_source.ref_file' | 26 --ref_file '$seq_data.seq_source.ref_file' |
28 #else: | 27 #else: |
29 --index '${seq_data.seq_source.index.fields.path}' | 28 --index '${seq_data.seq_source.index.fields.path}' |
30 #end if | 29 #end if |
31 #end if | 30 #end if |
32 | 31 |
33 $discard_single_exon | 32 $discard_single_exon |
34 | 33 |
35 -e $max_dist_exon | 34 -e $max_dist_exon |
36 -d $max_dist_group | 35 -d $max_dist_group |
37 | 36 |
38 #if $discard_intron_redundant_transfrags: | 37 #if $discard_intron_redundant_transfrags: |
39 -F | 38 -F |
40 #end if | 39 #end if |
41 | 40 |
42 ## Outputs. | 41 ## Outputs. |
43 --combined-transcripts '${transcripts_combined}' | 42 --combined-transcripts '${transcripts_combined}' |
44 | 43 |
45 @CUFFLINKS_GTF_INPUTS@ | 44 @CUFFLINKS_GTF_INPUTS@ |
46 </command> | 45 ]]></command> |
47 <inputs> | 46 <inputs> |
48 <expand macro="cufflinks_gtf_inputs" /> | 47 <expand macro="cufflinks_gtf_inputs" /> |
49 <conditional name="annotation"> | 48 <conditional name="annotation"> |
50 <param name="use_ref_annotation" type="select" label="Use Reference Annotation"> | 49 <param name="use_ref_annotation" type="select" label="Use Reference Annotation"> |
51 <option value="No">No</option> | 50 <option value="No">No</option> |
58 </when> | 57 </when> |
59 <when value="No"> | 58 <when value="No"> |
60 </when> | 59 </when> |
61 </conditional> | 60 </conditional> |
62 <conditional name="seq_data"> | 61 <conditional name="seq_data"> |
63 <param name="use_seq_data" type="select" label="Use Sequence Data" | 62 <param name="use_seq_data" type="select" label="Use Sequence Data" |
64 help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff."> | 63 help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff."> |
65 <option value="Yes">Yes</option> | 64 <option value="Yes">Yes</option> |
66 <option value="No">No</option> | 65 <option value="No">No</option> |
67 </param> | 66 </param> |
68 <when value="No"></when> | 67 <when value="No"></when> |
89 <param type="select" name="discard_single_exon" label="discard (ignore) single-exon transcripts"> | 88 <param type="select" name="discard_single_exon" label="discard (ignore) single-exon transcripts"> |
90 <option value="" selected="True">No</option> | 89 <option value="" selected="True">No</option> |
91 <option value="-M">Discard single-exon transfrags and reference transcripts</option> | 90 <option value="-M">Discard single-exon transfrags and reference transcripts</option> |
92 <option value="-N">Discard single-exon reference transcripts</option> | 91 <option value="-N">Discard single-exon reference transcripts</option> |
93 </param> | 92 </param> |
94 <param type="integer" name="max_dist_exon" value="100" label="Max. Distance for assessing exon accuracy" | 93 <param type="integer" name="max_dist_exon" value="100" label="Max. Distance for assessing exon accuracy" |
95 help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100" /> | 94 help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100" /> |
96 <param type="integer" name="max_dist_group" value="100" label="Max.Distance for transcript grouping" | 95 <param type="integer" name="max_dist_group" value="100" label="Max.Distance for transcript grouping" |
97 help="max. distance (range) for grouping transcript start sites. Default: 100" /> | 96 help="max. distance (range) for grouping transcript start sites. Default: 100" /> |
98 <param type="boolean" name="discard_intron_redundant_transfrags" label="discard intron-redundant transfrags sharing 5'" | 97 <param type="boolean" name="discard_intron_redundant_transfrags" label="discard intron-redundant transfrags sharing 5'" |
99 help="Discard intron-redundant transfrags if they share the 5' end (if they differ only at the 3' end)" /> | 98 help="Discard intron-redundant transfrags if they share the 5' end (if they differ only at the 3' end)" /> |
100 </inputs> | 99 </inputs> |
101 | 100 |
102 <outputs> | 101 <outputs> |
103 <data format="txt" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy" | 102 <data format="txt" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy" |
104 from_work_dir="cc_output.stats" /> | 103 from_work_dir="cc_output.stats" /> |
105 <data format="tabular" name="input1_tmap" label="${tool.name} on ${on_string}: data ${inputs[0].hid} tmap file" | 104 <data format="tabular" name="input1_tmap" label="${tool.name} on ${on_string}: data ${inputs[0].hid} tmap file" |
106 from_work_dir="cc_output.input1.tmap" /> | 105 from_work_dir="cc_output.input1.tmap" /> |
107 <data format="tabular" name="input1_refmap" | 106 <data format="tabular" name="input1_refmap" |
108 label="${tool.name} on ${on_string}: data ${inputs[0].hid} refmap file" | 107 label="${tool.name} on ${on_string}: data ${inputs[0].hid} refmap file" |
109 from_work_dir="cc_output.input1.refmap"> | 108 from_work_dir="cc_output.input1.refmap"> |
110 <filter>annotation['use_ref_annotation'] == 'Yes'</filter> | 109 <filter>annotation['use_ref_annotation'] == 'Yes'</filter> |
111 </data> | 110 </data> |
112 <data format="tabular" name="input2_tmap" label="${tool.name} on ${on_string}: data ${inputs[1].hid} tmap file" from_work_dir="cc_output.input2.tmap"> | 111 <data format="tabular" name="input2_tmap" label="${tool.name} on ${on_string}: data ${inputs[1].hid} tmap file" from_work_dir="cc_output.input2.tmap"> |
113 <filter>@HAS_MULTIPLE_INPUTS@</filter> | 112 <filter>@HAS_MULTIPLE_INPUTS@</filter> |
114 </data> | 113 </data> |
115 <data format="tabular" name="input2_refmap" | 114 <data format="tabular" name="input2_refmap" |
116 label="${tool.name} on ${on_string}: data ${inputs[1].hid} refmap file" | 115 label="${tool.name} on ${on_string}: data ${inputs[1].hid} refmap file" |
117 from_work_dir="cc_output.input2.refmap"> | 116 from_work_dir="cc_output.input2.refmap"> |
118 <filter>annotation['use_ref_annotation'] == 'Yes' and @HAS_MULTIPLE_INPUTS@</filter> | 117 <filter>annotation['use_ref_annotation'] == 'Yes' and @HAS_MULTIPLE_INPUTS@</filter> |
119 </data> | 118 </data> |
120 <data format="tabular" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking" from_work_dir="cc_output.tracking"> | 119 <data format="tabular" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking" from_work_dir="cc_output.tracking"> |
121 <filter>@HAS_MULTIPLE_INPUTS@</filter> | 120 <filter>@HAS_MULTIPLE_INPUTS@</filter> |
122 </data> | 121 </data> |
123 <data format="gtf" name="transcripts_combined" label="${tool.name} on ${on_string}: combined transcripts"/> | 122 <data format="gtf" name="transcripts_combined" label="${tool.name} on ${on_string}: combined transcripts"/> |
124 </outputs> | 123 </outputs> |
125 | 124 |
126 <tests> | 125 <tests> |
127 <!-- | 126 <!-- |
128 cuffcompare -r cuffcompare_in3.gtf -R cuffcompare_in1.gtf cuffcompare_in2.gtf | 127 cuffcompare -r cuffcompare_in3.gtf -R cuffcompare_in1.gtf cuffcompare_in2.gtf |
129 --> | 128 --> |
130 <test> | 129 <test> |
131 <param name="inputs" value="cuffcompare_in1.gtf,cuffcompare_in2.gtf" ftype="gtf"/> | 130 <param name="inputs" value="cuffcompare_in1.gtf,cuffcompare_in2.gtf" ftype="gtf"/> |
132 <param name="use_ref_annotation" value="Yes"/> | 131 <param name="use_ref_annotation" value="Yes"/> |
171 | 170 |
172 **Input format** | 171 **Input format** |
173 | 172 |
174 Cuffcompare takes Cufflinks' GTF output as input, and optionally can take a "reference" annotation (such as from Ensembl_) | 173 Cuffcompare takes Cufflinks' GTF output as input, and optionally can take a "reference" annotation (such as from Ensembl_) |
175 | 174 |
176 .. _Ensembl: http://www.ensembl.org | 175 .. _Ensembl: http://www.ensembl.org |
177 | 176 |
178 ------ | 177 ------ |
179 | 178 |
180 **Outputs** | 179 **Outputs** |
181 | 180 |
185 | 184 |
186 Cuffcompare reports various statistics related to the "accuracy" of the transcripts in each sample when compared to the reference annotation data. The typical gene finding measures of "sensitivity" and "specificity" (as defined in Burset, M., Guigó, R. : Evaluation of gene structure prediction programs (1996) Genomics, 34 (3), pp. 353-367. doi: 10.1006/geno.1996.0298) are calculated at various levels (nucleotide, exon, intron, transcript, gene) for each input file and reported in this file. The Sn and Sp columns show specificity and sensitivity values at each level, while the fSn and fSp columns are "fuzzy" variants of these same accuracy calculations, allowing for a very small variation in exon boundaries to still be counted as a "match". | 185 Cuffcompare reports various statistics related to the "accuracy" of the transcripts in each sample when compared to the reference annotation data. The typical gene finding measures of "sensitivity" and "specificity" (as defined in Burset, M., Guigó, R. : Evaluation of gene structure prediction programs (1996) Genomics, 34 (3), pp. 353-367. doi: 10.1006/geno.1996.0298) are calculated at various levels (nucleotide, exon, intron, transcript, gene) for each input file and reported in this file. The Sn and Sp columns show specificity and sensitivity values at each level, while the fSn and fSp columns are "fuzzy" variants of these same accuracy calculations, allowing for a very small variation in exon boundaries to still be counted as a "match". |
187 | 186 |
188 Transcripts Combined File: | 187 Transcripts Combined File: |
189 | 188 |
190 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. | 189 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. |
191 | 190 |
192 Transcripts Tracking File: | 191 Transcripts Tracking File: |
193 | 192 |
194 This file matches transcripts up between samples. Each row contains a transcript structure that is present in one or more input GTF files. Because the transcripts will generally have different IDs (unless you assembled your RNA-Seq reads against a reference transcriptome), cuffcompare examines the structure of each the transcripts, matching transcripts that agree on the coordinates and order of all of their introns, as well as strand. Matching transcripts are allowed to differ on the length of the first and last exons, since these lengths will naturally vary from sample to sample due to the random nature of sequencing. | 193 This file matches transcripts up between samples. Each row contains a transcript structure that is present in one or more input GTF files. Because the transcripts will generally have different IDs (unless you assembled your RNA-Seq reads against a reference transcriptome), cuffcompare examines the structure of each the transcripts, matching transcripts that agree on the coordinates and order of all of their introns, as well as strand. Matching transcripts are allowed to differ on the length of the first and last exons, since these lengths will naturally vary from sample to sample due to the random nature of sequencing. |
195 If you ran cuffcompare with the -r option, the first and second columns contain the closest matching reference transcript to the one described by each row. | 194 If you ran cuffcompare with the -r option, the first and second columns contain the closest matching reference transcript to the one described by each row. |
207 1 Cufflinks transfrag id TCONS_00000045 A unique internal id for the transfrag | 206 1 Cufflinks transfrag id TCONS_00000045 A unique internal id for the transfrag |
208 2 Cufflinks locus id XLOC_000023 A unique internal id for the locus | 207 2 Cufflinks locus id XLOC_000023 A unique internal id for the locus |
209 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 | 208 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 |
210 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 | 209 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 |
211 5 Class code c The type of match between the Cufflinks transcripts in column 6 and the reference transcript. See class codes | 210 5 Class code c The type of match between the Cufflinks transcripts in column 6 and the reference transcript. See class codes |
212 | 211 |
213 Each of the columns after the fifth have the following format: | 212 Each of the columns after the fifth have the following format: |
214 qJ:gene_id|transcript_id|FMI|FPKM|conf_lo|conf_hi | 213 qJ:gene_id|transcript_id|FMI|FPKM|conf_lo|conf_hi |
215 | 214 |
216 A transcript need be present in all samples to be reported in the tracking file. A sample not containing a transcript will have a "-" in its entry in the row for that transcript. | 215 A transcript need be present in all samples to be reported in the tracking file. A sample not containing a transcript will have a "-" in its entry in the row for that transcript. |
217 | 216 |
220 If you ran cuffcompare with the -r option, tracking rows will contain the following values. If you did not use -r, the rows will all contain "-" in their class code column:: | 219 If you ran cuffcompare with the -r option, tracking rows will contain the following values. If you did not use -r, the rows will all contain "-" in their class code column:: |
221 | 220 |
222 Priority Code Description | 221 Priority Code Description |
223 --------------------------------- | 222 --------------------------------- |
224 1 = Match | 223 1 = Match |
225 2 c Contained | 224 2 c Contained |
226 3 j New isoform | 225 3 j New isoform |
227 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. | 226 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. |
228 5 i A single exon transcript falling entirely with a reference intron | 227 5 i A single exon transcript falling entirely with a reference intron |
229 6 o Generic exonic overlap with a reference transcript | 228 6 o Generic exonic overlap with a reference transcript |
230 7 p Possible polymerase run-on fragment | 229 7 p Possible polymerase run-on fragment |
231 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 | 230 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 |
232 9 u Unknown, intergenic transcript | 231 9 u Unknown, intergenic transcript |
233 10 x Exonic overlap with reference on the opposite strand | 232 10 x Exonic overlap with reference on the opposite strand |
234 11 s An intron of the transfrag overlaps a reference intron on the opposite strand (likely due to read mapping errors) | 233 11 s An intron of the transfrag overlaps a reference intron on the opposite strand (likely due to read mapping errors) |
235 12 . (.tracking file only, indicates multiple classifications) | 234 12 . (.tracking file only, indicates multiple classifications) |
236 | 235 |
237 ------- | 236 ------- |
238 | 237 |
239 **Settings** | 238 **Settings** |
240 | 239 |
241 All of the options have a default value. You can change any of them. Most of the options in Cuffcompare have been implemented here. | 240 All of the options have a default value. You can change any of them. Most of the options in Cuffcompare have been implemented here. |