Mercurial > repos > iuc > idr_download_by_ids

comparison idr_download_by_ids.xml @ 4:11036f6197d6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
author iuc
date Fri, 15 May 2020 14:54:02 -0400
parents 381f248febba
children e08b1dc0480c
comparison
equal deleted inserted replaced
3:381f248febba 4:11036f6197d6
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="idr_download_by_ids" name="IDR Download" version="0.30" profile="18.09"> 2 <tool id="idr_download_by_ids" name="IDR Download" version="0.40" profile="18.09">
3 <description>- download images from the Image Data Resource using image IDs</description> 3 <description>- download images from the Image Data Resource using image IDs</description>
4 <macros> 4 <macros>
5 <xml name="region_spec" token_pos="upper-left corner"> 5 <xml name="region_spec" token_pos="upper-left corner">
6 <param name="x_coord" type="integer" value="0" min="0" 6 <param name="x_coord" type="integer" value="0" min="0"
7 label="x-coordinate of region @POS@" /> 7 label="x-coordinate of region @POS@" />
36 -z $z_section 36 -z $z_section
37 #if str($clip_image.select): 37 #if str($clip_image.select):
38 ${clip_image.select} ${clip_image.x_coord} ${clip_image.y_coord} ${clip_image.width} ${clip_image.height} 38 ${clip_image.select} ${clip_image.x_coord} ${clip_image.y_coord} ${clip_image.width} ${clip_image.height}
39 #end if 39 #end if
40 $skip_failed 40 $skip_failed
41 $download_tar
41 42
42 2> >(tee -a $out_log >&2) 43 2> >(tee -a $out_log >&2)
43 ]]></command> 44 ]]></command>
44 <inputs> 45 <inputs>
45 <conditional name="image_ids"> 46 <conditional name="image_ids">
84 </when> 85 </when>
85 </conditional> 86 </conditional>
86 <param name="skip_failed" type="boolean" checked="false" truevalue="--skip-failed" falsevalue="" 87 <param name="skip_failed" type="boolean" checked="false" truevalue="--skip-failed" falsevalue=""
87 label="Skip failed retrievals?" 88 label="Skip failed retrievals?"
88 help="By default the tool will fail with an error on the first non-retrievable image ID. Here, you can choose to skip non-retrievable image IDs and continue downloading the available ones instead. The error log will contain warnings about failed IDs in this case." /> 89 help="By default the tool will fail with an error on the first non-retrievable image ID. Here, you can choose to skip non-retrievable image IDs and continue downloading the available ones instead. The error log will contain warnings about failed IDs in this case." />
90 <param name="download_tar" type="boolean" checked="true" truevalue="--download-tar" falsevalue=""
91 label="Download images in a tarball?"
92 help="By default, the tool will download a tarball containing individual images into your Galaxy history. This option is strongly recommended, especially for a large number of files. With this option set to No, you will download a collection of images, only suggested for a small number of files." >
93 </param>
89 </inputs> 94 </inputs>
90 <outputs> 95 <outputs>
91 <data name="out_log" format="txt" label="${tool.name} error log" /> 96 <data name="out_log" format="txt" label="${tool.name} error log" />
92 <collection name="output_file" type="list"> 97 <collection name="output_file" type="list">
93 <discover_datasets pattern="__name_and_ext__" directory="downloads" /> 98 <discover_datasets pattern="__name_and_ext__" directory="downloads" />
99 <filter>not download_tar</filter>
94 </collection> 100 </collection>
101 <data name="output_tar" format="tar" from_work_dir="./downloads/images.tar" label ="Images tarball">
102 <filter>download_tar</filter>
103 </data>
95 </outputs> 104 </outputs>
96 <tests> 105 <tests>
97 <test> 106 <test>
98 <param name="source" value="dataset" /> 107 <param name="source" value="dataset" />
99 <param name="id_spec" value="ids.txt" /> 108 <param name="id_spec" value="ids.txt" />
104 <param name="y_coord" value="3" /> 113 <param name="y_coord" value="3" />
105 <param name="width" value="5" /> 114 <param name="width" value="5" />
106 <param name="height" value="5" /> 115 <param name="height" value="5" />
107 </conditional> 116 </conditional>
108 <param name="frame" value="2" /> 117 <param name="frame" value="2" />
118 <param name="download_tar" value="false" />
109 <output_collection name="output_file" type="list"> 119 <output_collection name="output_file" type="list">
110 <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test1.tiff"/> 120 <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test1.tiff"/>
111 </output_collection> 121 </output_collection>
112 </test> 122 </test>
113 <test> 123 <test>
120 <param name="y_coord" value="3" /> 130 <param name="y_coord" value="3" />
121 <param name="width" value="5" /> 131 <param name="width" value="5" />
122 <param name="height" value="5" /> 132 <param name="height" value="5" />
123 </conditional> 133 </conditional>
124 <param name="frame" value="2" /> 134 <param name="frame" value="2" />
135 <param name="download_tar" value="false" />
125 <output_collection name="output_file" type="list"> 136 <output_collection name="output_file" type="list">
126 <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test1.tiff"/> 137 <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test1.tiff"/>
127 </output_collection> 138 </output_collection>
128 </test> 139 </test>
129 <test> 140 <test>
136 <param name="y_coord" value="5" /> 147 <param name="y_coord" value="5" />
137 <param name="width" value="5" /> 148 <param name="width" value="5" />
138 <param name="height" value="5" /> 149 <param name="height" value="5" />
139 </conditional> 150 </conditional>
140 <param name="frame" value="2" /> 151 <param name="frame" value="2" />
152 <param name="download_tar" value="false" />
141 <output_collection name="output_file" type="list"> 153 <output_collection name="output_file" type="list">
142 <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test1.tiff"/> 154 <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test1.tiff"/>
143 </output_collection> 155 </output_collection>
144 </test> 156 </test>
145 <test> 157 <test>
149 <param name="z_section" value="4" /> 161 <param name="z_section" value="4" />
150 <conditional name="clip_image"> 162 <conditional name="clip_image">
151 <param name="select" value="" /> 163 <param name="select" value="" />
152 </conditional> 164 </conditional>
153 <param name="frame" value="20" /> 165 <param name="frame" value="20" />
166 <param name="download_tar" value="false" />
154 <output_collection name="output_file" type="list" count="3"> 167 <output_collection name="output_file" type="list" count="3">
155 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024"> 168 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024">
156 <assert_contents> 169 <assert_contents>
157 <has_size value="2097286" /> 170 <has_size value="2097286" />
158 </assert_contents> 171 </assert_contents>
173 <param name="z_section" value="4" /> 186 <param name="z_section" value="4" />
174 <conditional name="clip_image"> 187 <conditional name="clip_image">
175 <param name="select" value="" /> 188 <param name="select" value="" />
176 </conditional> 189 </conditional>
177 <param name="frame" value="20" /> 190 <param name="frame" value="20" />
191 <param name="download_tar" value="false" />
178 </test> 192 </test>
179 <test> 193 <test>
180 <!-- Repeat test with non-existing image-ID 9036708999, 194 <!-- Repeat test with non-existing image-ID 9036708999,
181 but use skip-failed option --> 195 but use skip-failed option -->
182 <param name="source" value="link" /> 196 <param name="source" value="link" />
186 <conditional name="clip_image"> 200 <conditional name="clip_image">
187 <param name="select" value="" /> 201 <param name="select" value="" />
188 </conditional> 202 </conditional>
189 <param name="frame" value="20" /> 203 <param name="frame" value="20" />
190 <param name="skip_failed" value="true" /> 204 <param name="skip_failed" value="true" />
205 <param name="download_tar" value="false" />
191 <output_collection name="output_file" type="list" count="2"> 206 <output_collection name="output_file" type="list" count="2">
192 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024"> 207 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024">
193 <assert_contents> 208 <assert_contents>
194 <has_size value="2097286" /> 209 <has_size value="2097286" />
195 </assert_contents> 210 </assert_contents>
199 <assert_contents> 214 <assert_contents>
200 <has_text text="9036708999: Unable to find an image with this ID in the database. Skipping download!" /> 215 <has_text text="9036708999: Unable to find an image with this ID in the database. Skipping download!" />
201 <has_text text="(ID: 9036710): Specified image plane (4) is out of bounds" /> 216 <has_text text="(ID: 9036710): Specified image plane (4) is out of bounds" />
202 <has_n_lines n="2"/> 217 <has_n_lines n="2"/>
203 </assert_contents> 218 </assert_contents>
219 </output>
220 </test>
221 <test>
222 <!-- Test for download images in a tarball -->
223 <param name="source" value="dataset" />
224 <param name="id_spec" value="ids_tar.txt" />
225 <param name="channel" value="Hoechst" />
226 <conditional name="clip_image">
227 <param name="select" value="--rectangle" />
228 <param name="x_coord" value="0" />
229 <param name="y_coord" value="0" />
230 <param name="width" value="671" />
231 <param name="height" value="511" />
232 </conditional>
233 <param name="frame" value="0" />
234 <output name="output_tar">
235 <assert_contents>
236 <has_size value="1382400" />
237 <has_archive_member path=".*/*__1828167__0__0__671__511.tiff" >
238 <has_size value="685884" />
239 </has_archive_member>
240 <has_archive_member path=".*/*__1828658__0__0__671__511.tiff" >
241 <has_size value="685884" />
242 </has_archive_member>
243 </assert_contents>
204 </output> 244 </output>
205 </test> 245 </test>
206 </tests> 246 </tests>
207 <help><![CDATA[ 247 <help><![CDATA[
208 Download image data from the IDR_ (Image Data Resource) - a public repository 248 Download image data from the IDR_ (Image Data Resource) - a public repository