Mercurial > repos > guerler > springsuite
comparison spring_minz.xml @ 12:0ea00dce62ab draft
"planemo upload commit 373d73ef3a09902e75f10084e30b271d84a6d7b1"
| author | guerler |
|---|---|
| date | Fri, 25 Sep 2020 19:39:11 +0000 |
| parents | 21a7dd67b483 |
| children | f8ba4dd48cbd |
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| 11:21a7dd67b483 | 12:0ea00dce62ab |
|---|---|
| 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 #for target in $targets | 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 | 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 | 12 #end for |
| 13 echo 0 | |
| 13 ]]></command> | 14 ]]></command> |
| 14 <inputs> | 15 <inputs> |
| 15 <param format="txt" name="targets" type="data_collection" label="Target Profiles" help="Homology search result of target/query profiles `hhr`."/> | 16 <param format="txt" name="targets" type="data_collection" label="Target Profiles" help="Homology search result of target/query 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`."/> | 17 <param format="txt" name="inputs" type="data_collection" collection_type="list" label="Input Profiles" help="Homology search results of input profiles `hhr`."/> |
| 17 <param format="txt" name="crossreference" type="data" label="Cross Reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/> | 18 <param format="txt" name="crossreference" type="data" label="Cross Reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/> |
| 23 </outputs> | 24 </outputs> |
| 24 <tests> | 25 <tests> |
| 25 <test> | 26 <test> |
| 26 <param name="targets"> | 27 <param name="targets"> |
| 27 <collection type="list"> | 28 <collection type="list"> |
| 29 <element name="6W4H_A.hhr" value="6W4H_A.hhr" /> | |
| 30 <element name="6W4H_B.hhr" value="6W4H_B.hhr" /> | |
| 31 <element name="6W9C_A.hhr" value="6W9C_A.hhr" /> | |
| 32 <element name="6W9Q_A.hhr" value="6W9Q_A.hhr" /> | |
| 33 <element name="6W37_A.hhr" value="6W37_A.hhr" /> | |
| 34 <element name="6WEY_A.hhr" value="6WEY_A.hhr" /> | |
| 35 <element name="6WJI_A.hhr" value="6WJI_A.hhr" /> | |
| 36 <element name="6WLC_A.hhr" value="6WLC_A.hhr" /> | |
| 28 <element name="7BQY_A.hhr" value="7BQY_A.hhr" /> | 37 <element name="7BQY_A.hhr" value="7BQY_A.hhr" /> |
| 29 </collection> | 38 </collection> |
| 30 </param> | 39 </param> |
| 31 <param name="idx" value="10"/> | 40 <param name="idx" value="10"/> |
| 32 <param name="inputs"> | 41 <param name="inputs"> |
| 33 <collection type="list"> | 42 <collection type="list"> |
| 34 <element name="6W37_A.hhr" value="6W37_A.hhr" /> | |
| 35 <element name="6W4H_A.hhr" value="6W4H_A.hhr" /> | 43 <element name="6W4H_A.hhr" value="6W4H_A.hhr" /> |
| 36 <element name="6W4H_B.hhr" value="6W4H_B.hhr" /> | 44 <element name="6W4H_B.hhr" value="6W4H_B.hhr" /> |
| 37 <element name="6W9C_A.hhr" value="6W9C_A.hhr" /> | 45 <element name="6W9C_A.hhr" value="6W9C_A.hhr" /> |
| 38 <element name="6W9Q_A.hhr" value="6W9Q_A.hhr" /> | 46 <element name="6W9Q_A.hhr" value="6W9Q_A.hhr" /> |
| 47 <element name="6W37_A.hhr" value="6W37_A.hhr" /> | |
| 39 <element name="6WEY_A.hhr" value="6WEY_A.hhr" /> | 48 <element name="6WEY_A.hhr" value="6WEY_A.hhr" /> |
| 40 <element name="6WJI_A.hhr" value="6WJI_A.hhr" /> | 49 <element name="6WJI_A.hhr" value="6WJI_A.hhr" /> |
| 41 <element name="6WLC_A.hhr" value="6WLC_A.hhr" /> | 50 <element name="6WLC_A.hhr" value="6WLC_A.hhr" /> |
| 51 <element name="7BQY_A.hhr" value="7BQY_A.hhr" /> | |
| 42 </collection> | 52 </collection> |
| 43 </param> | 53 </param> |
| 44 <param name="crossreference" value="dbCAN_random.txt"/> | 54 <param name="crossreference" value="dbCAN_random.txt"/> |
| 45 <output name="output" file="dbCAN_result.txt"/> | 55 <output name="output" file="dbCAN_result.txt"/> |
| 46 </test> | 56 </test> |