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comparison reheader.xml @ 23:5db0545b9004 draft

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update to v0.1.7.3
author wolma
date Thu, 21 Jul 2016 03:55:49 -0400
parents c46406466625
children
comparison
equal deleted inserted replaced
22:24154c580718 23:5db0545b9004
1 <tool id="reheader" name="Reheader BAM file" version="0.1.7.2"> 1 <tool id="reheader" name="Reheader BAM file" version="0.1.7.3">
2 <description>From a BAM file generate a new file with the original header (if any) replaced or modified by that found in a second SAM file</description> 2 <description>From a BAM file generate a new file with the original header (if any) replaced or modified by that found in a second SAM file</description>
3 <expand macro="requirements"/> 3 <expand macro="requirements" />
4 <version_command>python3 -m MiModD version -q</version_command> 4 <version_command>python3 -m MiModD version -q</version_command>
5 <command> 5 <command>
6 #if ($str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form") or $str($co.treat_co) != "ignore": 6 #if ($str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form") or $str($co.treat_co) != "ignore":
7 python3 -m MiModD header 7 python3 -m MiModD header
8 #if $str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form": 8 #if $str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form":
101 101
102 <macros> 102 <macros>
103 <import>toolshed_macros.xml</import> 103 <import>toolshed_macros.xml</import>
104 <macro name="getreadgroupinfo"> 104 <macro name="getreadgroupinfo">
105 <conditional name="rginfo"> 105 <conditional name="rginfo">
106 <param name="source" type="select" label="source of new read-group information" help=""> 106 <param help="" label="source of new read-group information" name="source" type="select">
107 <option value="from_file">existing SAM file</option> 107 <option value="from_file">existing SAM file</option>
108 <option value="from_form">input form</option> 108 <option value="from_form">input form</option>
109 </param> 109 </param>
110 <when value="from_file"> 110 <when value="from_file">
111 <param name="data" type="data" format="sam" label="read-group template file in SAM format" help="use the read group information found in this file" /> 111 <param format="sam" help="use the read group information found in this file" label="read-group template file in SAM format" name="data" type="data" />
112 <repeat name="rg" title="custom read-group mapping" default="0" min="0" help="read-group information found in the input file, by default, gets updated / replaced with information from template file read-groups with matching IDs. Alternatively, you may specify explicit read-group mappings below."> 112 <repeat default="0" help="read-group information found in the input file, by default, gets updated / replaced with information from template file read-groups with matching IDs. Alternatively, you may specify explicit read-group mappings below." min="0" name="rg" title="custom read-group mapping">
113 <param name="source_id" type="text" label="modify input file information for read-group ID (will create the read-group if it does not exist)" /> 113 <param label="modify input file information for read-group ID (will create the read-group if it does not exist)" name="source_id" type="text" />
114 <param name="rg_id" type="text" label="with template file information for read-group ID" /> 114 <param label="with template file information for read-group ID" name="rg_id" type="text" />
115 </repeat> 115 </repeat>
116 </when> 116 </when>
117 <when value="from_form"> 117 <when value="from_form">
118 <repeat name="rg" title="new read-group info" default="1" min="1"> 118 <repeat default="1" min="1" name="rg" title="new read-group info">
119 <param name="source_id" type="text" label="read-group ID (will create the read-group if it does not exist)" help="required field" /> 119 <param help="required field" label="read-group ID (will create the read-group if it does not exist)" name="source_id" type="text" />
120 <param name="rg_id" type="hidden" value="" /> 120 <param name="rg_id" type="hidden" value="" />
121 <param name="rg_sm" type="text" label="sample name" help="required field" /> 121 <param help="required field" label="sample name" name="rg_sm" type="text" />
122 <param name="rg_ds" type="text" label="description" /> 122 <param label="description" name="rg_ds" type="text" />
123 <param name="rg_date" type="text" label="date (YY-MM-DD format) the run was produced" /> 123 <param label="date (YY-MM-DD format) the run was produced" name="rg_date" type="text" />
124 <param name="rg_cn" type="text" label="name of sequencing center" /> 124 <param label="name of sequencing center" name="rg_cn" type="text" />
125 <param name="rg_lb" type="text" label="read-group library" /> 125 <param label="read-group library" name="rg_lb" type="text" />
126 <param name="rg_pl" type="text" label="platform/technology used to produce the reads" /> 126 <param label="platform/technology used to produce the reads" name="rg_pl" type="text" />
127 <param name="rg_pi" type="text" label="predicted median insert size" /> 127 <param label="predicted median insert size" name="rg_pi" type="text" />
128 <param name="rg_pu" type="text" label="platform unit; unique identifier" /> 128 <param label="platform unit; unique identifier" name="rg_pu" type="text" />
129 </repeat> 129 </repeat>
130 </when> 130 </when>
131 </conditional> 131 </conditional>
132 </macro> 132 </macro>
133 </macros> 133 </macros>
134 134
135 <inputs> 135 <inputs>
136 136
137 <param name="inputfile" type="data" format="bam" label="input file in BAM format" help="the file to reheader." /> 137 <param format="bam" help="the file to reheader." label="input file in BAM format" name="inputfile" type="data" />
138 138
139 <conditional name="rg"> 139 <conditional name="rg">
140 <param name="treat_rg" type="select" label="modify read-group information ?" help="Replace mode will ignore ALL existing read group information in the input file and use ONLY template information, Update mode will COPY existing input file information and UPDATE it with template information; choose No, ... to leave read-group information alone."> 140 <param help="Replace mode will ignore ALL existing read group information in the input file and use ONLY template information, Update mode will COPY existing input file information and UPDATE it with template information; choose No, ... to leave read-group information alone." label="modify read-group information ?" name="treat_rg" type="select">
141 <option value="ignore">No, do not change read-groups.</option> 141 <option value="ignore">No, do not change read-groups.</option>
142 <option value="update">Yes, update existing information</option> 142 <option value="update">Yes, update existing information</option>
143 <option value="replace">Yes, replace existing information</option> 143 <option value="replace">Yes, replace existing information</option>
144 </param> 144 </param>
145 <when value="update"> 145 <when value="update">
149 <expand macro="getreadgroupinfo" /> 149 <expand macro="getreadgroupinfo" />
150 </when> 150 </when>
151 </conditional> 151 </conditional>
152 152
153 <conditional name="co"> 153 <conditional name="co">
154 <param name="treat_co" type="select" label="modify comments in the input file ?" help=""> 154 <param help="" label="modify comments in the input file ?" name="treat_co" type="select">
155 <option value="ignore">No, do not change comments.</option> 155 <option value="ignore">No, do not change comments.</option>
156 <option value="update">Yes, append new comments to existing ones</option> 156 <option value="update">Yes, append new comments to existing ones</option>
157 <option value="replace">Yes, replace all existing comments</option> 157 <option value="replace">Yes, replace all existing comments</option>
158 </param> 158 </param>
159 <when value="update"> 159 <when value="update">
160 <repeat name="coinfo" title="comment line" default="0" min="0"> 160 <repeat default="0" min="0" name="coinfo" title="comment line">
161 <param name="line" type="text" size="80" /> 161 <param name="line" size="80" type="text" />
162 </repeat> 162 </repeat>
163 </when> 163 </when>
164 <when value="replace"> 164 <when value="replace">
165 <repeat name="coinfo" title="comment line" default="0" min="0"> 165 <repeat default="0" min="0" name="coinfo" title="comment line">
166 <param name="line" type="text" size="80" /> 166 <param name="line" size="80" type="text" />
167 </repeat> 167 </repeat>
168 </when> 168 </when>
169 </conditional> 169 </conditional>
170 170
171 <repeat name="rg_renaming" title="rename read-group" default="0" min="0" help="Warning: changing read-group IDs may increase job runtime substantially."> 171 <repeat default="0" help="Warning: changing read-group IDs may increase job runtime substantially." min="0" name="rg_renaming" title="rename read-group">
172 <param name="from" type="text" size="30" label="old name" help="as it appears in the current input file header"/> 172 <param help="as it appears in the current input file header" label="old name" name="from" size="30" type="text" />
173 <param name="to" type="text" size="30" label="new name" /> 173 <param label="new name" name="to" size="30" type="text" />
174 </repeat> 174 </repeat>
175 175
176 <repeat name="sq_renaming" title="rename sequence" default="0" min="0" help="Warning: changing sequence names may increase job runtime substantially."> 176 <repeat default="0" help="Warning: changing sequence names may increase job runtime substantially." min="0" name="sq_renaming" title="rename sequence">
177 <param name="from" type="text" size="30" label="old name" help="as it appears in the current input file header"/> 177 <param help="as it appears in the current input file header" label="old name" name="from" size="30" type="text" />
178 <param name="to" type="text" size="30" label="new name" /> 178 <param label="new name" name="to" size="30" type="text" />
179 </repeat> 179 </repeat>
180 180
181 </inputs> 181 </inputs>
182 182
183 <outputs> 183 <outputs>
184 <data name="output" format="bam" label="(Re)headered bam file from MiModd ${tool.name} on ${on_string}"> 184 <data format="bam" label="(Re)headered bam file from MiModd ${tool.name} on ${on_string}" name="output">
185 </data> 185 </data>
186 </outputs> 186 </outputs>
187 187
188 <help> 188 <help>
189 .. class:: infomark 189 .. class:: infomark
198 198
199 The template information used to modify or replace the input file metadata is provided through forms or, in the case of read-group information, can be taken from an existing SAM file as can be generated, for example, with the *NGS Run Annotation* tool. 199 The template information used to modify or replace the input file metadata is provided through forms or, in the case of read-group information, can be taken from an existing SAM file as can be generated, for example, with the *NGS Run Annotation* tool.
200 200
201 </help> 201 </help>
202 </tool> 202 </tool>
203