Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/tests/wf/trick_revsort.cwl @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 #!/usr/bin/env cwl-runner |
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2 # |
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3 # This is a two-step workflow which uses "revtool" and "sorttool" defined above. |
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4 # |
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5 class: Workflow |
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6 doc: "Reverse the lines in a document, then sort those lines." |
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7 cwlVersion: v1.0 |
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8 |
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9 # Requirements & hints specify prerequisites and extensions to the workflow. |
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10 # In this example, DockerRequirement specifies a default Docker container |
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11 # in which the command line tools will execute. |
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12 hints: |
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13 - class: DockerRequirement |
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14 dockerPull: debian:8 |
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15 |
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16 |
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17 # The inputs array defines the structure of the input object that describes |
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18 # the inputs to the workflow. |
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19 # |
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20 # The "reverse_sort" input parameter demonstrates the "default" field. If the |
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21 # field "reverse_sort" is not provided in the input object, the default value will |
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22 # be used. |
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23 inputs: |
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24 workflow_input: |
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25 type: File |
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26 doc: "The input file to be processed." |
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27 format: iana:text/plain |
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28 default: |
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29 class: File |
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30 location: hello.txt |
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31 reverse_sort: |
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32 type: boolean |
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33 default: true |
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34 doc: "If true, reverse (decending) sort" |
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35 name: |
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36 type: string |
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37 doc: "Here to test for a bug in --pack" |
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38 |
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39 # The "outputs" array defines the structure of the output object that describes |
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40 # the outputs of the workflow. |
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41 # |
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42 # Each output field must be connected to the output of one of the workflow |
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43 # steps using the "outputSource" field. Here, the parameter "sorted_output" of the |
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44 # workflow comes from the "sorted_output" output of the "sorted" step. |
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45 outputs: |
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46 sorted_output: |
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47 type: File |
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48 outputSource: sorted/sorted_output |
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49 doc: "The output with the lines reversed and sorted." |
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50 |
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51 # The "steps" array lists the executable steps that make up the workflow. |
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52 # The tool to execute each step is listed in the "run" field. |
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53 # |
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54 # In the first step, the "in" field of the step connects the upstream |
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55 # parameter "workflow_input" of the workflow to the input parameter of the tool |
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56 # "revtool_input" |
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57 # |
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58 # In the second step, the "in" field of the step connects the output |
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59 # parameter "revtool_output" from the first step to the input parameter of the |
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60 # tool "sorted_input". |
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61 steps: |
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62 rev: |
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63 in: |
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64 revtool_input: workflow_input |
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65 out: [revtool_output] |
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66 run: revtool.cwl |
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67 |
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68 sorted: |
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69 in: |
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70 sorted_input: rev/revtool_output |
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71 reverse: reverse_sort |
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72 out: [sorted_output] |
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73 run: sorttool.cwl |
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74 |
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75 $namespaces: |
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76 iana: https://www.iana.org/assignments/media-types/ |
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77 |
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78 $schemas: |
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79 - empty2.ttl |