Mercurial > repos > iuc > medaka_variant_pipeline

comparison medaka_variant.xml @ 2:ce2bf68a260d draft

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"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
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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>