Mercurial > repos > devteam > cufflinks
comparison cufflinks_wrapper.xml @ 12:d080005cffe1 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
author | iuc |
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date | Tue, 16 Jun 2020 13:00:32 -0400 |
parents | e04dbae2abe0 |
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11:e04dbae2abe0 | 12:d080005cffe1 |
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1 <tool id="cufflinks" name="Cufflinks" version="@VERSION@.2"> | 1 <tool id="cufflinks" name="Cufflinks" version="@VERSION@.3"> |
2 <description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description> | 2 <description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</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>cufflinks 2>&1 | head -n 1</version_command> | 7 <requirement type="package" version="3.6">python</requirement> |
8 <command detect_errors="aggressive"> | 8 </expand> |
9 python '$__tool_directory__/cufflinks_wrapper.py' | 9 <version_command><![CDATA[cufflinks 2>&1 | head -n 1]]></version_command> |
10 --input '$input' | 10 <command detect_errors="aggressive"><![CDATA[ |
11 --assembled-isoforms-output '$assembled_isoforms' | 11 cufflinks -q --no-update-check |
12 '$input' | |
12 --num-threads "\${GALAXY_SLOTS:-4}" | 13 --num-threads "\${GALAXY_SLOTS:-4}" |
13 -I $max_intron_len | 14 -I $max_intron_len |
14 -F $min_isoform_fraction | 15 -F $min_isoform_fraction |
15 -j $pre_mrna_fraction | 16 -j $pre_mrna_fraction |
16 $length_correction | 17 $length_correction |
29 | 30 |
30 ## Bias correction? | 31 ## Bias correction? |
31 #if $bias_correction.do_bias_correction == "Yes": | 32 #if $bias_correction.do_bias_correction == "Yes": |
32 -b | 33 -b |
33 #if $bias_correction.seq_source.index_source == "history": | 34 #if $bias_correction.seq_source.index_source == "history": |
34 --ref_file '$bias_correction.seq_source.ref_file' | 35 '$bias_correction.seq_source.ref_file' |
35 #else: | 36 #else: |
36 --index '${bias_correction.seq_source.index.fields.path}' | 37 '${bias_correction.seq_source.index.fields.path}' |
37 #end if | 38 #end if |
38 #end if | 39 #end if |
39 | 40 |
40 ## Multi-read correct? | 41 ## Multi-read correct? |
41 #if str($multiread_correct) == "Yes": | 42 $multiread_correct |
42 -u | 43 |
43 #end if | |
44 | |
45 ## Include global model if available. | |
46 #if $global_model: | |
47 --global_model '$global_model' | |
48 #end if | |
49 | |
50 ## advanced settings | 44 ## advanced settings |
51 #if $advanced_settings.use_advanced_settings == "Yes": | 45 #if $advanced_settings.use_advanced_settings == "Yes": |
52 --library-type $advanced_settings.library_type | 46 --library-type $advanced_settings.library_type |
53 #if $advanced_settings.mask_file: | 47 #if $advanced_settings.mask_file: |
54 --mask-file '$advanced_settings.mask_file' | 48 --mask-file '$advanced_settings.mask_file' |
55 #end if | 49 #end if |
56 --inner-mean-dist $advanced_settings.inner_mean_dist | 50 --frag-len-mean $advanced_settings.inner_mean_dist |
57 --inner-dist-std-dev $advanced_settings.inner_dist_std_dev | 51 --frag-len-std-dev $advanced_settings.inner_dist_std_dev |
58 --max-mle-iterations $advanced_settings.max_mle_iterations | 52 --max-mle-iterations $advanced_settings.max_mle_iterations |
59 --junc-alpha $advanced_settings.junc_alpha | 53 --junc-alpha $advanced_settings.junc_alpha |
60 --small-anchor-fraction $advanced_settings.small_anchor_fraction | 54 --small-anchor-fraction $advanced_settings.small_anchor_fraction |
61 --overhang-tolerance $advanced_settings.overhang_tolerance | 55 --overhang-tolerance $advanced_settings.overhang_tolerance |
62 --max-bundle-length $advanced_settings.max_bundle_length | 56 --max-bundle-length $advanced_settings.max_bundle_length |
63 --max-bundle-frags $advanced_settings.max_bundle_frags | 57 --max-bundle-frags $advanced_settings.max_bundle_frags |
64 --min-intron-length $advanced_settings.min_intron_length | 58 --min-intron-length $advanced_settings.min_intron_length |
65 --trim-3-avgcov-thresh $advanced_settings.trim_three_avgcov_thresh | 59 --trim-3-avgcov-thresh $advanced_settings.trim_three_avgcov_thresh |
66 --trim-3-dropoff-frac $advanced_settings.trim_three_dropoff_frac | 60 --trim-3-dropoff-frac $advanced_settings.trim_three_dropoff_frac |
67 #end if | 61 #end if |
68 </command> | 62 2> stderr |
63 | |
64 && python '$__tool_directory__/mass.py' stderr '$global_model' "transcripts.gtf" | |
65 ]]></command> | |
69 <inputs> | 66 <inputs> |
70 <param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/> | 67 <param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/> |
71 <param name="max_intron_len" type="integer" value="300000" min="1" max="600000" label="Max Intron Length" help="ignore alignments with gaps longer than this"/> | 68 <param name="max_intron_len" type="integer" value="300000" min="1" max="600000" label="Max Intron Length" help="ignore alignments with gaps longer than this"/> |
72 <param name="min_isoform_fraction" type="float" value="0.10" min="0" max="1" label="Min Isoform Fraction" help="suppress transcripts below this abundance level"/> | 69 <param name="min_isoform_fraction" type="float" value="0.10" min="0" max="1" label="Min Isoform Fraction" help="suppress transcripts below this abundance level"/> |
73 <param name="pre_mrna_fraction" type="float" value="0.15" min="0" max="1" label="Pre MRNA Fraction" help="suppress intra-intronic transcripts below this level"/> | 70 <param name="pre_mrna_fraction" type="float" value="0.15" min="0" max="1" label="Pre MRNA Fraction" help="suppress intra-intronic transcripts below this level"/> |
123 </conditional> | 120 </conditional> |
124 </when> | 121 </when> |
125 <when value="No" /> | 122 <when value="No" /> |
126 </conditional> | 123 </conditional> |
127 | 124 |
128 <param name="multiread_correct" type="select" label="Use multi-read correct" | 125 <param name="multiread_correct" type="boolean" label="Use multi-read correct" |
129 help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome."> | 126 truevalue="-u" falsevalue="" checked="false" |
130 <option value="No" selected="true">No</option> | 127 help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome."/> |
131 <option value="Yes">Yes</option> | |
132 </param> | |
133 | 128 |
134 <param name="length_correction" type="select" label="Apply length correction" help="Mode of length normalization to transcript FPKM."> | 129 <param name="length_correction" type="select" label="Apply length correction" help="Mode of length normalization to transcript FPKM."> |
135 <option value="" selected="true">Cufflinks Effective Length Correction</option> | 130 <option value="" selected="true">Cufflinks Effective Length Correction</option> |
136 <option value="--no-effective-length-correction">Standard Length Correction</option> | 131 <option value="--no-effective-length-correction">Standard Length Correction</option> |
137 <option value="--no-length-correction">No Length Correction at all (use raw counts)</option> | 132 <option value="--no-length-correction">No Length Correction at all (use raw counts)</option> |
173 </conditional> | 168 </conditional> |
174 </inputs> | 169 </inputs> |
175 <outputs> | 170 <outputs> |
176 <data format="tabular" name="genes_expression" label="${tool.name} on ${on_string}: gene expression" from_work_dir="genes.fpkm_tracking"/> | 171 <data format="tabular" name="genes_expression" label="${tool.name} on ${on_string}: gene expression" from_work_dir="genes.fpkm_tracking"/> |
177 <data format="tabular" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression" from_work_dir="isoforms.fpkm_tracking"/> | 172 <data format="tabular" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression" from_work_dir="isoforms.fpkm_tracking"/> |
178 <data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts"/> | 173 <data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts" from_work_dir="transcripts.gtf"/> |
179 <data format="txt" name="total_map_mass" label="${tool.name} on ${on_string}: total map mass" hidden="true" from_work_dir="global_model.txt"/> | 174 <data format="txt" name="total_map_mass" label="${tool.name} on ${on_string}: total map mass" hidden="true" from_work_dir="global_model.txt"/> |
180 <data format="gtf" name="skipped" label="${tool.name} on ${on_string}: Skipped Transcripts" from_work_dir="skipped.gtf"/> | 175 <data format="gtf" name="skipped" label="${tool.name} on ${on_string}: Skipped Transcripts" from_work_dir="skipped.gtf"/> |
181 </outputs> | 176 </outputs> |
182 | 177 |
183 <trackster_conf> | 178 <trackster_conf> |
198 <param name="length_correction" value=""/> | 193 <param name="length_correction" value=""/> |
199 <param name="use_advanced_settings" value="No" /> | 194 <param name="use_advanced_settings" value="No" /> |
200 <output name="genes_expression" ftype="tabular" lines_diff="2" file="cufflinks_out3.fpkm_tracking"/> | 195 <output name="genes_expression" ftype="tabular" lines_diff="2" file="cufflinks_out3.fpkm_tracking"/> |
201 <output name="transcripts_expression" ftype="tabular" lines_diff="2" file="cufflinks_out2.fpkm_tracking"/> | 196 <output name="transcripts_expression" ftype="tabular" lines_diff="2" file="cufflinks_out2.fpkm_tracking"/> |
202 <output name="assembled_isoforms" file="cufflinks_out1.gtf"/> | 197 <output name="assembled_isoforms" file="cufflinks_out1.gtf"/> |
203 <output name="global_model" file="cufflinks_out4.txt"/> | 198 <output name="total_map_mass" file="cufflinks_out4.txt"/> |
204 <output name="skipped" file="cufflinks_out4.gtf"/> | 199 <output name="skipped" file="cufflinks_out4.gtf"/> |
205 </test> | 200 </test> |
206 </tests> | 201 </tests> |
207 | 202 |
208 <help> | 203 <help> |
296 -F After calculating isoform abundance for a gene, Cufflinks filters out transcripts that it believes are very low abundance, because isoforms expressed at extremely low levels often cannot reliably be assembled, and may even be artifacts of incompletely spliced precursors of processed transcripts. This parameter is also used to filter out introns that have far fewer spliced alignments supporting them. The default is 0.05, or 5% of the most abundant isoform (the major isoform) of the gene. | 291 -F After calculating isoform abundance for a gene, Cufflinks filters out transcripts that it believes are very low abundance, because isoforms expressed at extremely low levels often cannot reliably be assembled, and may even be artifacts of incompletely spliced precursors of processed transcripts. This parameter is also used to filter out introns that have far fewer spliced alignments supporting them. The default is 0.05, or 5% of the most abundant isoform (the major isoform) of the gene. |
297 -j Some RNA-Seq protocols produce a significant amount of reads that originate from incompletely spliced transcripts, and these reads can confound the assembly of fully spliced mRNAs. Cufflinks uses this parameter to filter out alignments that lie within the intronic intervals implied by the spliced alignments. The minimum depth of coverage in the intronic region covered by the alignment is divided by the number of spliced reads, and if the result is lower than this parameter value, the intronic alignments are ignored. The default is 5%. | 292 -j Some RNA-Seq protocols produce a significant amount of reads that originate from incompletely spliced transcripts, and these reads can confound the assembly of fully spliced mRNAs. Cufflinks uses this parameter to filter out alignments that lie within the intronic intervals implied by the spliced alignments. The minimum depth of coverage in the intronic region covered by the alignment is divided by the number of spliced reads, and if the result is lower than this parameter value, the intronic alignments are ignored. The default is 5%. |
298 -G Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript. | 293 -G Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript. |
299 -N With this option, Cufflinks excludes the contribution of the top 25 percent most highly expressed genes from the number of mapped fragments used in the FPKM denominator. This can improve robustness of differential expression calls for less abundant genes and transcripts. | 294 -N With this option, Cufflinks excludes the contribution of the top 25 percent most highly expressed genes from the number of mapped fragments used in the FPKM denominator. This can improve robustness of differential expression calls for less abundant genes and transcripts. |
300 </help> | 295 </help> |
301 <citations> | 296 <expand macro="citations"/> |
302 <citation type="doi">10.1038/nbt.1621</citation> | |
303 </citations> | |
304 </tool> | 297 </tool> |