Mercurial > repos > artbio > concatenate_multiple_datasets

comparison catWrapper.xml @ 2:1fe4d165ac0e draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 9f8e7a0dfea7761d71b9f2963f4686b4e892c2cf
author artbio
date Mon, 15 Apr 2019 18:52:43 -0400
parents 3a4694d4354f
children 62aebaf6cfa0
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1:3a4694d4354f 2:1fe4d165ac0e
1 <tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.0"> 1 <tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.1.0">
2 <description>tail-to-head by specifying how</description> 2 <description>tail-to-head by specifying how</description>
3 <command><![CDATA[ 3 <command><![CDATA[
4 #if $headers == 0: 4 #if $headers == 0:
5 #set $concat_command = "cat" 5 #set $concat_command = "cat"
6 #else: 6 #else:
54 mkdir concatenated && 54 mkdir concatenated &&
55 #if $dataset_names == "No": 55 #if $dataset_names == "No":
56 #for $file in $global_condition.inputs.keys() 56 #for $file in $global_condition.inputs.keys()
57 $concat_command 57 $concat_command
58 $global_condition.inputs[$file]['forward'] 58 $global_condition.inputs[$file]['forward']
59 > concatenated/'${file}.${global_condition.inputs[$file]['reverse'].ext}.listed' && 59 > concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
60 $concat_command 60 $concat_command
61 $global_condition.inputs[$file]['reverse'] 61 $global_condition.inputs[$file]['reverse']
62 >> concatenated/'${file}.${global_condition.inputs[$file]['reverse'].ext}.listed' && 62 >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
63 #end for 63 #end for
64 sleep 1 64 sleep 1
65 #else: 65 #else:
66 #for $file in $global_condition.inputs.keys() 66 #for $file in $global_condition.inputs.keys()
67 printf "# ${file}_forward\n" > concatenated/'${file}.${global_condition.inputs[$file]['reverse'].ext}.listed' && 67 printf "# ${file}_forward\n" > concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
68 $concat_command 68 $concat_command
69 $global_condition.inputs[$file]['forward'] 69 $global_condition.inputs[$file]['forward']
70 >> concatenated/'${file}.${global_condition.inputs[$file]['reverse'].ext}.listed' && 70 >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
71 printf "# ${file}_reverse\n" >> concatenated/'${file}.${global_condition.inputs[$file]['reverse'].ext}.listed' && 71 printf "# ${file}_reverse\n" >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
72 $concat_command 72 $concat_command
73 $global_condition.inputs[$file]['reverse'] 73 $global_condition.inputs[$file]['reverse']
74 >> concatenated/'${file}.${global_condition.inputs[$file]['reverse'].ext}.listed' && 74 >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
75 #end for 75 #end for
76 sleep 1 76 sleep 1
77 #end if 77 #end if
78 #else if $global_condition.paired_cat_type == "all": 78 #else if $global_condition.paired_cat_type == "all":
79 #if $dataset_names == "No": 79 #if $dataset_names == "No":
132 <data name="forward" /> 132 <data name="forward" />
133 <data name="reverse" /> 133 <data name="reverse" />
134 <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_strand'</filter> 134 <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_strand'</filter>
135 </collection> 135 </collection>
136 <collection name="list_output" type="list" label="Concatenation by pairs"> 136 <collection name="list_output" type="list" label="Concatenation by pairs">
137 <discover_datasets pattern="(?P&lt;name&gt;.*)\.(?P&lt;ext&gt;[^\._]+\.?[^\._])\.listed" visible="false" directory="concatenated"/> 137 <discover_datasets pattern="(?P&lt;name&gt;.*)\.listed\.(?P&lt;ext&gt;.*)\.listed" visible="false" directory="concatenated"/>
138 <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_pair'</filter> 138 <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_pair'</filter>
139 </collection> 139 </collection>
140 </outputs> 140 </outputs>
141 <tests> 141 <tests>
142 <!-- Single files concatenation --> 142 <!-- Single files concatenation -->