Mercurial > repos > iuc > medaka_variant_pipeline
comparison medaka_variant.xml @ 2:ce2bf68a260d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 7fec11af843c91c70413844368c1d5f5f78ce45e"
| author | iuc |
|---|---|
| date | Thu, 18 Jun 2020 05:08:40 -0400 |
| parents | 92cdc29a8620 |
| children | 148f32860445 |
comparison
equal
deleted
inserted
replaced
| 1:92cdc29a8620 | 2:ce2bf68a260d |
|---|---|
| 20 #end if | 20 #end if |
| 21 -o results | 21 -o results |
| 22 -s $s | 22 -s $s |
| 23 -m $m | 23 -m $m |
| 24 -t \${GALAXY_SLOTS:-4} | 24 -t \${GALAXY_SLOTS:-4} |
| 25 -p | |
| 25 -b $b | 26 -b $b |
| 26 -N $N | 27 -N $N |
| 27 -P $P | 28 -P $P |
| 28 $U | 29 $U |
| 29 $S | 30 $S |
| 51 <option value="round_0_hap_mixed_unphased_vcf">round_0_hap_mixed_unphased.vcf</option> | 52 <option value="round_0_hap_mixed_unphased_vcf">round_0_hap_mixed_unphased.vcf</option> |
| 52 <option value="round_1_hap_1_vcf">round_1_hap_1.vcf</option> | 53 <option value="round_1_hap_1_vcf">round_1_hap_1.vcf</option> |
| 53 <option value="round_1_hap_2_vcf">round_1_hap_2.vcf</option> | 54 <option value="round_1_hap_2_vcf">round_1_hap_2.vcf</option> |
| 54 <option value="round_1_hap_1_probs_hdf">round_1_hap_1_probs.hdf</option> | 55 <option value="round_1_hap_1_probs_hdf">round_1_hap_1_probs.hdf</option> |
| 55 <option value="round_1_hap_2_probs_hdf">round_1_hap_2_probs.hdf</option> | 56 <option value="round_1_hap_2_probs_hdf">round_1_hap_2_probs.hdf</option> |
| 57 <option value="round_1_phased.vcf">round_1_phased.vcf</option> | |
| 56 <option value="round_1_unfiltered_vcf">round_1_unfiltered.vcf</option> | 58 <option value="round_1_unfiltered_vcf">round_1_unfiltered.vcf</option> |
| 57 <option value="round_1_vcf" selected="true">round_1.vcf</option> | 59 <option value="round_1_vcf" selected="true">round_1.vcf</option> |
| 58 <option value="log">Log</option> | 60 <option value="log">Log</option> |
| 59 </param> | 61 </param> |
| 60 </inputs> | 62 </inputs> |
| 61 <outputs> | 63 <outputs> |
| 62 <!-- standard --> | 64 <!-- standard output--> |
| 63 <data name="out_round_1_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1.vcf" from_work_dir="results/round_1.vcf"> | 65 <data name="out_round_1_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1.vcf" from_work_dir="results/round_1.vcf"> |
| 64 <filter>'round_1_vcf' in out</filter> | 66 <filter>'round_1_vcf' in out</filter> |
| 65 </data> | 67 </data> |
| 66 <!-- optional --> | 68 <!-- optional output: round 0 --> |
| 67 <data name="out_round_0_hap_mixed_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_0_hap_mixed_probs_hdf" from_work_dir="results/round_0_hap_mixed_probs.hdf"> | 69 <data name="out_round_0_hap_mixed_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_0_hap_mixed_probs_hdf" from_work_dir="results/round_0_hap_mixed_probs.hdf"> |
| 68 <filter>'round_0_hap_mixed_probs_hdf' in out</filter> | 70 <filter>'round_0_hap_mixed_probs_hdf' in out</filter> |
| 69 </data> | 71 </data> |
| 70 <data name="out_round_0_hap_mixed_phased_bam" format="bam" label="${tool.name} on ${on_string}: round_0_hap_mixed_phased_bam" from_work_dir="results/round_0_hap_mixed_phased.bam"> | 72 <data name="out_round_0_hap_mixed_phased_bam" format="bam" label="${tool.name} on ${on_string}: round_0_hap_mixed_phased_bam" from_work_dir="results/round_0_hap_mixed_phased.bam"> |
| 71 <filter>'round_0_hap_mixed_phased_bam' in out</filter> | 73 <filter>'round_0_hap_mixed_phased_bam' in out</filter> |
| 74 <filter>'round_0_hap_mixed_phased_vcf' in out</filter> | 76 <filter>'round_0_hap_mixed_phased_vcf' in out</filter> |
| 75 </data> | 77 </data> |
| 76 <data name="out_round_0_hap_mixed_unphased_vcf" format="vcf" label="${tool.name} on ${on_string}: round_0_hap_mixed_unphased_vcf" from_work_dir="results/round_0_hap_mixed_unphased.vcf"> | 78 <data name="out_round_0_hap_mixed_unphased_vcf" format="vcf" label="${tool.name} on ${on_string}: round_0_hap_mixed_unphased_vcf" from_work_dir="results/round_0_hap_mixed_unphased.vcf"> |
| 77 <filter>'round_0_hap_mixed_unphased_vcf' in out</filter> | 79 <filter>'round_0_hap_mixed_unphased_vcf' in out</filter> |
| 78 </data> | 80 </data> |
| 79 <!-- round 1 --> | 81 <!-- optional output: round 1 --> |
| 80 <data name="out_round_1_hap_1_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_hap_1.vcf" from_work_dir="results/round_1_hap_1.vcf"> | 82 <data name="out_round_1_hap_1_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_hap_1.vcf" from_work_dir="results/round_1_hap_1.vcf"> |
| 81 <filter>'round_1_hap_1_vcf' in out</filter> | 83 <filter>'round_1_hap_1_vcf' in out</filter> |
| 82 </data> | 84 </data> |
| 83 <data name="out_round_1_hap_1_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_1_hap_1_probs.hdf" from_work_dir="results/round_1_hap_1_probs.hdf"> | 85 <data name="out_round_1_hap_1_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_1_hap_1_probs.hdf" from_work_dir="results/round_1_hap_1_probs.hdf"> |
| 84 <filter>'round_1_hap_1_probs_hdf' in out</filter> | 86 <filter>'round_1_hap_1_probs_hdf' in out</filter> |
| 87 <filter>'round_1_hap_2_vcf' in out</filter> | 89 <filter>'round_1_hap_2_vcf' in out</filter> |
| 88 </data> | 90 </data> |
| 89 <data name="out_round_1_hap_2_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_1_hap_2_probs.hdf" from_work_dir="results/round_1_hap_2_probs.hdf"> | 91 <data name="out_round_1_hap_2_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_1_hap_2_probs.hdf" from_work_dir="results/round_1_hap_2_probs.hdf"> |
| 90 <filter>'round_1_hap_2_probs_hdf' in out</filter> | 92 <filter>'round_1_hap_2_probs_hdf' in out</filter> |
| 91 </data> | 93 </data> |
| 94 <data name="out_round_1_phased.vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_phased.vcf" from_work_dir="results/round_1_phased.vcf"> | |
| 95 <filter>'round_1_phased.vcf' in out</filter> | |
| 96 </data> | |
| 92 <data name="out_round_1_unfiltered_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_unfiltered.vcf" from_work_dir="results/round_1_unfiltered.vcf"> | 97 <data name="out_round_1_unfiltered_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_unfiltered.vcf" from_work_dir="results/round_1_unfiltered.vcf"> |
| 93 <filter>'round_1_unfiltered_vcf' in out</filter> | 98 <filter>'round_1_unfiltered_vcf' in out</filter> |
| 94 </data> | 99 </data> |
| 100 <!-- optional output: log --> | |
| 95 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log"> | 101 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log"> |
| 96 <filter>'log' in out</filter> | 102 <filter>'log' in out</filter> |
| 97 </data> | 103 </data> |
| 98 </outputs> | 104 </outputs> |
| 99 <tests> | 105 <tests> |
| 139 - reads aligned to reference (BAM), should be aligned to the reference against which to call variants | 145 - reads aligned to reference (BAM), should be aligned to the reference against which to call variants |
| 140 - reference (FASTA) | 146 - reference (FASTA) |
| 141 | 147 |
| 142 **Output** | 148 **Output** |
| 143 | 149 |
| 150 - round_0_hap_mixed_phased.bam | |
| 144 - round_0_hap_mixed_phased.vcf | 151 - round_0_hap_mixed_phased.vcf |
| 145 - round_0_hap_mixed_probs.hdf | 152 - round_0_hap_mixed_probs.hdf |
| 146 - round_0_hap_mixed_unphased.vcf | 153 - round_0_hap_mixed_unphased.vcf |
| 147 - round_1_hap_1_probs.hdf | 154 - round_1_hap_1_probs.hdf |
| 148 - round_1_hap_1.vcf | 155 - round_1_hap_1.vcf |
| 149 - round_1_hap_2_probs.hdf | 156 - round_1_hap_2_probs.hdf |
| 150 - round_1_hap_2.vcf | 157 - round_1_hap_2.vcf |
| 158 - round_1_phased.vcf | |
| 151 - round_1_unfiltered.vcf | 159 - round_1_unfiltered.vcf |
| 152 - round_1.vcf | 160 - round_1.vcf |
| 161 - log | |
| 153 | 162 |
| 154 **References** | 163 **References** |
| 155 | 164 |
| 156 @REFERENCES@ | 165 @REFERENCES@ |
| 157 ]]></help> | 166 ]]></help> |