Mercurial > repos > iuc > medaka_variant_pipeline

comparison medaka_variant.xml @ 13:3fbefde449bc draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
author iuc
date Thu, 18 Nov 2021 20:01:04 +0000
parents 7623e5888be9
children
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12:597407d61386 13:3fbefde449bc
1 <tool id="medaka_variant_pipeline" name="medaka variant pipeline" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 1 <tool id="medaka_variant_pipeline" name="medaka variant pipeline" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>via neural networks</description> 2 <description>via neural networks</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
89 <filter>'round_1_hap_2_vcf' in out</filter> 89 <filter>'round_1_hap_2_vcf' in out</filter>
90 </data> 90 </data>
91 <data name="out_round_1_hap_2_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_1_hap_2_probs.hdf" from_work_dir="results/round_1_hap_2_probs.hdf"> 91 <data name="out_round_1_hap_2_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_1_hap_2_probs.hdf" from_work_dir="results/round_1_hap_2_probs.hdf">
92 <filter>'round_1_hap_2_probs_hdf' in out</filter> 92 <filter>'round_1_hap_2_probs_hdf' in out</filter>
93 </data> 93 </data>
94 <data name="out_round_1_phased.vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_phased.vcf" from_work_dir="results/round_1_phased.vcf"> 94 <data name="out_round_1_phased_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_phased.vcf" from_work_dir="results/round_1_phased.vcf">
95 <filter>'round_1_phased.vcf' in out</filter> 95 <filter>'round_1_phased.vcf' in out</filter>
96 </data> 96 </data>
97 <data name="out_round_1_unfiltered_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_unfiltered.vcf" from_work_dir="results/round_1_unfiltered.vcf"> 97 <data name="out_round_1_unfiltered_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_unfiltered.vcf" from_work_dir="results/round_1_unfiltered.vcf">
98 <filter>'round_1_unfiltered_vcf' in out</filter> 98 <filter>'round_1_unfiltered_vcf' in out</filter>
99 </data> 99 </data>
136 136
137 @WID@ 137 @WID@
138 138
139 The module *medaka_variant* performs a variant calling via neural networks. 139 The module *medaka_variant* performs a variant calling via neural networks.
140 140
141 ----
142
143 .. class:: infomark
144
141 **Input** 145 **Input**
142 146
143 It is unlikely that the model arguments should be changed from their defaults. 147 It is unlikely that the model arguments should be changed from their defaults.
144 148
145 - reads aligned to reference (BAM), should be aligned to the reference against which to call variants 149 - reads aligned to reference (BAM), should be aligned to the reference against which to call variants
146 - reference (FASTA) 150 - reference (FASTA)
151
152 ----
153
154 .. class:: infomark
147 155
148 **Output** 156 **Output**
149 157
150 - round_0_hap_mixed_phased.bam 158 - round_0_hap_mixed_phased.bam
151 - round_0_hap_mixed_phased.vcf 159 - round_0_hap_mixed_phased.vcf
158 - round_1_phased.vcf 166 - round_1_phased.vcf
159 - round_1_unfiltered.vcf 167 - round_1_unfiltered.vcf
160 - round_1.vcf 168 - round_1.vcf
161 - log 169 - log
162 170
171 @MODELS@
172
173 ----
174
175 .. class:: infomark
176
163 **References** 177 **References**
164 178
165 @REFERENCES@ 179 @REFERENCES@
166 ]]></help> 180 ]]></help>
167 <expand macro="citations"/> 181 <expand macro="citations"/>