Mercurial > repos > devteam > cuffcompare
comparison cuffcompare_wrapper.xml @ 10:f648e5180e40 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
author | iuc |
---|---|
date | Tue, 16 Jun 2020 12:59:38 -0400 |
parents | e66b9b5b8580 |
children |
comparison
equal
deleted
inserted
replaced
9:e66b9b5b8580 | 10:f648e5180e40 |
---|---|
1 <tool id="cuffcompare" name="Cuffcompare" version="@VERSION@.1"> | 1 <tool id="cuffcompare" name="Cuffcompare" version="@VERSION@.2"> |
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 <version_command>cuffcompare 2>&1 | head -n 1</version_command> | 7 <version_command><![CDATA[ |
8 cuffcompare 2>&1 | head -n 1 | |
9 ]]></version_command> | |
8 <command detect_errors="aggressive"><![CDATA[ | 10 <command detect_errors="aggressive"><![CDATA[ |
9 python '$__tool_directory__/cuffcompare_wrapper.py' | 11 @CUFFLINKS_LINK_GTF_INPUTS@ |
12 cuffcompare | |
13 -o output | |
10 ## Use annotation reference? | 14 ## Use annotation reference? |
11 #if $annotation.use_ref_annotation == "Yes": | 15 #if $annotation.use_ref_annotation == "Yes": |
12 -r '$annotation.reference_annotation' | 16 -r '$annotation.reference_annotation' |
13 #if $annotation.ignore_nonoverlapping_reference: | 17 #if $annotation.ignore_nonoverlapping_reference: |
14 -R | 18 -R |
15 #end if | 19 #end if |
16 #if $annotation.ignore_nonoverlapping_transfrags: | 20 #if $annotation.ignore_nonoverlapping_transfrags: |
17 -Q | 21 -Q |
18 #end if | 22 #end if |
19 | |
20 #end if | 23 #end if |
21 | 24 |
22 ## Use sequence data? | 25 ## Use sequence data? |
23 #if $seq_data.use_seq_data == "Yes": | 26 #if $seq_data.use_seq_data == "Yes": |
24 -s | 27 -s |
25 #if $seq_data.seq_source.index_source == "history": | 28 #if $seq_data.seq_source.index_source == "history": |
26 --ref_file '$seq_data.seq_source.ref_file' | 29 '$seq_data.seq_source.ref_file' |
27 #else: | 30 #else: |
28 --index '${seq_data.seq_source.index.fields.path}' | 31 '${seq_data.seq_source.index.fields.path}' |
29 #end if | 32 #end if |
30 #end if | 33 #end if |
31 | 34 |
32 $discard_single_exon | 35 $discard_single_exon |
33 | 36 |
34 -e $max_dist_exon | 37 -e $max_dist_exon |
35 -d $max_dist_group | 38 -d $max_dist_group |
36 | 39 |
37 #if $discard_intron_redundant_transfrags: | 40 $discard_intron_redundant_transfrags |
38 -F | |
39 #end if | |
40 | |
41 ## Outputs. | |
42 --combined-transcripts '${transcripts_combined}' | |
43 | 41 |
44 @CUFFLINKS_GTF_INPUTS@ | 42 @CUFFLINKS_GTF_INPUTS@ |
45 ]]></command> | 43 ]]></command> |
46 <inputs> | 44 <inputs> |
47 <expand macro="cufflinks_gtf_inputs" /> | 45 <expand macro="cufflinks_gtf_inputs" /> |
48 <conditional name="annotation"> | 46 <conditional name="annotation"> |
49 <param name="use_ref_annotation" type="select" label="Use Reference Annotation"> | 47 <param name="use_ref_annotation" type="select" label="Use Reference Annotation"> |
50 <option value="No">No</option> | 48 <option value="No">No</option> |
84 </when> | 82 </when> |
85 </conditional> | 83 </conditional> |
86 </when> | 84 </when> |
87 </conditional> | 85 </conditional> |
88 <param type="select" name="discard_single_exon" label="discard (ignore) single-exon transcripts"> | 86 <param type="select" name="discard_single_exon" label="discard (ignore) single-exon transcripts"> |
89 <option value="" selected="True">No</option> | 87 <option value="" selected="True">No</option> |
90 <option value="-M">Discard single-exon transfrags and reference transcripts</option> | 88 <option value="-M">Discard single-exon transfrags and reference transcripts</option> |
91 <option value="-N">Discard single-exon reference transcripts</option> | 89 <option value="-N">Discard single-exon reference transcripts</option> |
92 </param> | 90 </param> |
93 <param type="integer" name="max_dist_exon" value="100" label="Max. Distance for assessing exon accuracy" | 91 <param type="integer" name="max_dist_exon" value="100" label="Max. Distance for assessing exon accuracy" |
94 help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100" /> | 92 help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100" /> |
95 <param type="integer" name="max_dist_group" value="100" label="Max.Distance for transcript grouping" | 93 <param type="integer" name="max_dist_group" value="100" label="Max.Distance for transcript grouping" |
96 help="max. distance (range) for grouping transcript start sites. Default: 100" /> | 94 help="max. distance (range) for grouping transcript start sites. Default: 100" /> |
97 <param type="boolean" name="discard_intron_redundant_transfrags" label="discard intron-redundant transfrags sharing 5'" | 95 <param type="boolean" name="discard_intron_redundant_transfrags" label="discard intron-redundant transfrags sharing 5'" |
96 value="false" truevalue="-F" falsevalue="" | |
98 help="Discard intron-redundant transfrags if they share the 5' end (if they differ only at the 3' end)" /> | 97 help="Discard intron-redundant transfrags if they share the 5' end (if they differ only at the 3' end)" /> |
99 </inputs> | 98 </inputs> |
100 | 99 |
101 <outputs> | 100 <outputs> |
102 <data format="txt" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy" | 101 <data format="txt" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy" |
103 from_work_dir="cc_output.stats" /> | 102 from_work_dir="output.stats" /> |
104 <data format="tabular" name="input1_tmap" label="${tool.name} on ${on_string}: data ${inputs[0].hid} tmap file" | 103 <data format="tabular" name="input1_tmap" label="${tool.name} on ${on_string}: data ${inputs[0].hid} tmap file" |
105 from_work_dir="cc_output.input1.tmap" /> | 104 from_work_dir="output.input_0.tmap" /> |
106 <data format="tabular" name="input1_refmap" | 105 <data format="tabular" name="input1_refmap" |
107 label="${tool.name} on ${on_string}: data ${inputs[0].hid} refmap file" | 106 label="${tool.name} on ${on_string}: data ${inputs[0].hid} refmap file" |
108 from_work_dir="cc_output.input1.refmap"> | 107 from_work_dir="output.input_0.refmap"> |
109 <filter>annotation['use_ref_annotation'] == 'Yes'</filter> | 108 <filter>annotation['use_ref_annotation'] == 'Yes'</filter> |
110 </data> | 109 </data> |
111 <data format="tabular" name="input2_tmap" label="${tool.name} on ${on_string}: data ${inputs[1].hid} tmap file" from_work_dir="cc_output.input2.tmap"> | 110 <data format="tabular" name="input2_tmap" label="${tool.name} on ${on_string}: data ${inputs[1].hid} tmap file" from_work_dir="output.input_1.tmap"> |
112 <filter>@HAS_MULTIPLE_INPUTS@</filter> | 111 <filter>@HAS_MULTIPLE_INPUTS@</filter> |
113 </data> | 112 </data> |
114 <data format="tabular" name="input2_refmap" | 113 <data format="tabular" name="input2_refmap" |
115 label="${tool.name} on ${on_string}: data ${inputs[1].hid} refmap file" | 114 label="${tool.name} on ${on_string}: data ${inputs[1].hid} refmap file" |
116 from_work_dir="cc_output.input2.refmap"> | 115 from_work_dir="output.input_1.refmap"> |
117 <filter>annotation['use_ref_annotation'] == 'Yes' and @HAS_MULTIPLE_INPUTS@</filter> | 116 <filter>annotation['use_ref_annotation'] == 'Yes' and @HAS_MULTIPLE_INPUTS@</filter> |
118 </data> | 117 </data> |
119 <data format="tabular" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking" from_work_dir="cc_output.tracking"> | 118 <data format="tabular" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking" from_work_dir="output.tracking"> |
120 <filter>@HAS_MULTIPLE_INPUTS@</filter> | 119 <filter>@HAS_MULTIPLE_INPUTS@</filter> |
121 </data> | 120 </data> |
122 <data format="gtf" name="transcripts_combined" label="${tool.name} on ${on_string}: combined transcripts"/> | 121 <data format="gtf" name="transcripts_combined" label="${tool.name} on ${on_string}: combined transcripts" from_work_dir="output.combined.gtf"/> |
123 </outputs> | 122 </outputs> |
124 | 123 |
125 <tests> | 124 <tests> |
126 <!-- | 125 <!-- |
127 cuffcompare -r cuffcompare_in3.gtf -R cuffcompare_in1.gtf cuffcompare_in2.gtf | 126 cuffcompare -r cuffcompare_in3.gtf -R cuffcompare_in1.gtf cuffcompare_in2.gtf |
128 --> | 127 --> |
129 <test> | 128 <test expect_num_outputs="7"> |
130 <param name="inputs" value="cuffcompare_in1.gtf,cuffcompare_in2.gtf" ftype="gtf"/> | 129 <param name="inputs" value="cuffcompare_in1.gtf,cuffcompare_in2.gtf" ftype="gtf"/> |
131 <param name="use_ref_annotation" value="Yes"/> | 130 <param name="use_ref_annotation" value="Yes"/> |
132 <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/> | 131 <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/> |
133 <param name="ignore_nonoverlapping_reference" value="Yes"/> | 132 <param name="ignore_nonoverlapping_reference" value="Yes"/> |
134 <param name="ignore_nonoverlapping_transfrags" value="No"/> | 133 <param name="ignore_nonoverlapping_transfrags" value="No"/> |
135 <param name="use_seq_data" value="No"/> | 134 <param name="use_seq_data" value="No"/> |
136 <param name="discard_single_exon" value="" /> | 135 <param name="discard_single_exon" value="" /> |
137 <param name="max_dist_exon" value="100" /> | 136 <param name="max_dist_exon" value="100" /> |
138 <param name="max_dist_group" value="100" /> | 137 <param name="max_dist_group" value="100" /> |
139 <param name="discard_intron_redundant_transfrags" value="No" /> | 138 <param name="discard_intron_redundant_transfrags" value="false" /> |
140 <!-- Line diffs are the result of different locations for input files; this cannot be fixed as cuffcompare outputs | 139 <!-- Line diffs are the result of different locations for input files; this cannot be fixed as cuffcompare outputs |
141 full input path for each input. --> | 140 full input path for each input. --> |
142 <output name="transcripts_accuracy" file="cuffcompare_out7.txt" lines_diff="2"/> | 141 <output name="transcripts_accuracy" file="cuffcompare_out7.txt" lines_diff="6"/> |
143 <output name="input1_tmap" file="cuffcompare_out1.tmap"/> | 142 <output name="input1_tmap" file="cuffcompare_out1.tmap"/> |
144 <output name="input1_refmap" file="cuffcompare_out2.refmap"/> | 143 <output name="input1_refmap" file="cuffcompare_out2.refmap"/> |
145 <output name="input2_tmap" file="cuffcompare_out3.tmap"/> | 144 <output name="input2_tmap" file="cuffcompare_out3.tmap"/> |
146 <output name="input2_refmap" file="cuffcompare_out4.refmap"/> | 145 <output name="input2_refmap" file="cuffcompare_out4.refmap"/> |
147 <output name="transcripts_tracking" file="cuffcompare_out6.tracking"/> | 146 <output name="transcripts_tracking" file="cuffcompare_out6.tracking"/> |
246 This is a list of implemented Cuffcompare options:: | 245 This is a list of implemented Cuffcompare options:: |
247 | 246 |
248 -r An optional "reference" annotation GTF. Each sample is matched against this file, and sample isoforms are tagged as overlapping, matching, or novel where appropriate. See the refmap and tmap output file descriptions below. | 247 -r An optional "reference" annotation GTF. Each sample is matched against this file, and sample isoforms are tagged as overlapping, matching, or novel where appropriate. See the refmap and tmap output file descriptions below. |
249 -R If -r was specified, this option causes cuffcompare to ignore reference transcripts that are not overlapped by any transcript in one of cuff1.gtf,...,cuffN.gtf. Useful for ignoring annotated transcripts that are not present in your RNA-Seq samples and thus adjusting the "sensitivity" calculation in the accuracy report written in the transcripts_accuracy file | 248 -R If -r was specified, this option causes cuffcompare to ignore reference transcripts that are not overlapped by any transcript in one of cuff1.gtf,...,cuffN.gtf. Useful for ignoring annotated transcripts that are not present in your RNA-Seq samples and thus adjusting the "sensitivity" calculation in the accuracy report written in the transcripts_accuracy file |
250 </help> | 249 </help> |
251 <citations> | 250 <expand macro="citations"/> |
252 <citation type="doi">10.1038/nbt.1621</citation> | |
253 </citations> | |
254 </tool> | 251 </tool> |