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comparison spring_minz.xml @ 11:21a7dd67b483 draft

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"planemo upload commit f208fb81425711754738fc8e612ee2d5cc26377f"
author guerler
date Fri, 25 Sep 2020 19:07:14 +0000
parents 860bd6f8f480
children 0ea00dce62ab
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10:860bd6f8f480 11:21a7dd67b483
5 mkdir -p inputs && 5 mkdir -p inputs &&
6 #for input in $inputs 6 #for input in $inputs
7 link '${str(input)}' 'inputs/${input.element_identifier}' && 7 link '${str(input)}' 'inputs/${input.element_identifier}' &&
8 echo '${input.element_identifier}' >> 'input_list' && 8 echo '${input.element_identifier}' >> 'input_list' &&
9 #end for 9 #end for
10 python3 '$__tool_directory__/spring_minz.py' -m '$minscore' -t '$target' -c '$crossreference' -x '$idx' -o '$output' -l input_list -i inputs 10 #for target in $targets
11 python3 '$__tool_directory__/spring_minz.py' -m '$minscore' -t '${str(target)}' -n '${target.element_identifier}' -c '$crossreference' -x '$idx' -o '$output' -l input_list -i inputs
12 #end for
11 ]]></command> 13 ]]></command>
12 <inputs> 14 <inputs>
13 <param format="txt" name="target" type="data" label="Target Profile" help="Homology search result of target/query profile `hhr`."/> 15 <param format="txt" name="targets" type="data_collection" label="Target Profiles" help="Homology search result of target/query profiles `hhr`."/>
14 <param format="txt" name="inputs" type="data_collection" collection_type="list" label="Input Profiles" help="Homology search results of input profiles `hhr`."/> 16 <param format="txt" name="inputs" type="data_collection" collection_type="list" label="Input Profiles" help="Homology search results of input profiles `hhr`."/>
15 <param format="txt" name="crossreference" type="data" label="Cross Reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/> 17 <param format="txt" name="crossreference" type="data" label="Cross Reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/>
16 <param name="minscore" type="integer" label="min-Z score threshold" value="10" min="1" max="100" help="Matching interaction pairs with a score lower than this threshold will be excluded."/> 18 <param name="minscore" type="integer" label="min-Z score threshold" value="10" min="1" max="100" help="Matching interaction pairs with a score lower than this threshold will be excluded."/>
17 <param name="idx" type="integer" label="Identifier length" value="6" min="1" max="20" help="Specify the length of the identifier e.g. `1ACB_A` has length 6."/> 19 <param name="idx" type="integer" label="Identifier length" value="6" min="1" max="20" help="Specify the length of the identifier e.g. `1ACB_A` has length 6."/>
18 </inputs> 20 </inputs>
19 <outputs> 21 <outputs>
20 <data format="txt" name="output" /> 22 <data format="txt" name="output" />
21 </outputs> 23 </outputs>
22 <tests> 24 <tests>
23 <test> 25 <test>
24 <param name="target" value="7BQY_A.hhr"/> 26 <param name="targets">
27 <collection type="list">
28 <element name="7BQY_A.hhr" value="7BQY_A.hhr" />
29 </collection>
30 </param>
25 <param name="idx" value="10"/> 31 <param name="idx" value="10"/>
26 <param name="inputs"> 32 <param name="inputs">
27 <collection type="list"> 33 <collection type="list">
28 <element name="6W37_A.hhr" value="6W37_A.hhr" /> 34 <element name="6W37_A.hhr" value="6W37_A.hhr" />
29 <element name="6W4H_A.hhr" value="6W4H_A.hhr" /> 35 <element name="6W4H_A.hhr" value="6W4H_A.hhr" />
37 </param> 43 </param>
38 <param name="crossreference" value="dbCAN_random.txt"/> 44 <param name="crossreference" value="dbCAN_random.txt"/>
39 <output name="output" file="dbCAN_result.txt"/> 45 <output name="output" file="dbCAN_result.txt"/>
40 </test> 46 </test>
41 <test> 47 <test>
42 <param name="target" value="NP_000282.1.hhr"/> 48 <param name="targets">
49 <collection type="list">
50 <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" />
51 </collection>
52 </param>
43 <param name="inputs"> 53 <param name="inputs">
44 <collection type="list"> 54 <collection type="list">
45 <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" /> 55 <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" />
46 <element name="NP_000290.2.hhr" value="NP_000290.2.hhr" /> 56 <element name="NP_000290.2.hhr" value="NP_000290.2.hhr" />
47 <element name="NP_000548.2.hhr" value="NP_000548.2.hhr" /> 57 <element name="NP_000548.2.hhr" value="NP_000548.2.hhr" />