{ "name": "Cool Test Workflow", "history_id": "8f7a155755f10e73", "step_version_changes": [], "version": 9, "steps": [ { "inputs": [ { "multiple": false, "help": "", "optional": false, "argument": null, "value": null, "label": "", "is_dynamic": false, "extensions": [ "data" ], "model_class": "DataCollectionToolParameter", "hidden": false, "refresh_on_change": true, "type": "data_collection", "options": { "hdca": [], "hda": [] }, "name": "input" } ], "step_index": 0, "replacement_parameters": [], "step_type": "data_collection_input", "output_connections": [ { "input_step_index": 2, "input_name": "inputs", "output_step_index": 0, "output_name": "output" }, { "input_step_index": 1, "input_name": "inputs_0|input", "output_step_index": 0, "output_name": "output" } ], "step_name": "Input dataset collection", "step_label": null, "step_version": null }, { "help": "

This tool takes two lists and creates a single unified list.

\n

This tool will create new history datasets for your collection but your quota usage will not increase.

\n", "labels": [], "panel_section_id": "collection_operations", "sharable_url": null, "id": "__MERGE_COLLECTION__", "step_label": "", "job_remap": false, "errors": {}, "requirements": [], "job_id": null, "citations": false, "post_job_actions": [], "form_style": "regular", "output_connections": [], "step_index": 1, "version": "1.0.0", "state_inputs": { "inputs": "[{\"__index__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input\": {\"__class__\": \"RuntimeValue\"}}]", "advanced": "{\"conflict\": {\"__current_case__\": 3, \"duplicate_options\": \"keep_first\"}}" }, "step_version": "1.0.0", "inputs": [ { "inputs": [ { "multiple": false, "help": "", "optional": false, "argument": null, "value": null, "label": "Input Collection", "is_dynamic": false, "extensions": [ "data" ], "model_class": "DataCollectionToolParameter", "hidden": false, "refresh_on_change": true, "type": "data_collection", "options": { "hdca": [], "hda": [] }, "name": "input" } ], "help": null, "title": "Input Collections", "default": 2, "max": "__Infinity__", "cache": { "0": [ { "default_value": null, "multiple": false, "help": "", "text_value": "Not available.", "optional": false, "argument": null, "value": { "__class__": "ConnectedValue" }, "label": "Input Collection", "is_dynamic": false, "extensions": [ "data" ], "model_class": "DataCollectionToolParameter", "hidden": false, "refresh_on_change": true, "type": "data_collection", "options": { "hdca": [], "hda": [] }, "name": "input" } ], "1": [ { "default_value": null, "multiple": false, "help": "", "text_value": "Not available.", "optional": false, "argument": null, "value": { "__class__": "RuntimeValue" }, "label": "Input Collection", "is_dynamic": false, "extensions": [ "data" ], "model_class": "DataCollectionToolParameter", "hidden": false, "refresh_on_change": true, "type": "data_collection", "options": { "hdca": [], "hda": [] }, "name": "input" } ] }, "min": 2, "model_class": "Repeat", "type": "repeat", "name": "inputs" }, { "inputs": [ { "test_param": { "multiple": false, "help": "Collection elements must have unique element identifiers, when appending how should unique identifiers be assured.", "display": null, "text_value": "Keep first instance", "argument": null, "value": "keep_first", "label": "How should conflicts (or potential conflicts) be handled?", "is_dynamic": false, "optional": false, "textable": true, "model_class": "SelectToolParameter", "hidden": false, "refresh_on_change": true, "type": "select", "options": [ [ "Append suffix to conflicted element identifers", "suffix_conflict", false ], [ "Append suffix to conflicted element identifers after first one encountered", "suffix_conflict_rest", false ], [ "Append suffix to every element identifer", "suffix_every", false ], [ "Keep first instance", "keep_first", true ], [ "Keep last instance", "keep_last", false ], [ "Fail collection creation", "fail", false ] ], "name": "duplicate_options" }, "model_class": "Conditional", "cases": [ { "model_class": "ConditionalWhen", "value": "suffix_conflict", "inputs": [ { "default_value": "_#", "help": "Describe the suffix pattern to use when joing element name and data copy number. For instance, the default is '_#', which will produce _1 as the first suffix used.", "area": false, "datalist": [], "text_value": "_#", "argument": null, "value": "_#", "label": "Use the follow suffix pattern:", "is_dynamic": false, "optional": false, "model_class": "TextToolParameter", "hidden": false, "refresh_on_change": false, "type": "text", "name": "suffix_pattern" } ] }, { "model_class": "ConditionalWhen", "value": "suffix_conflict_rest", "inputs": [ { "default_value": "_#", "help": "Describe the suffix pattern to use when joing element name and data copy number. For instance, the default is '_#', which will produce _1 as the first suffix used.", "area": false, "datalist": [], "text_value": "_#", "argument": null, "value": "_#", "label": "Use the follow suffix pattern:", "is_dynamic": false, "optional": false, "model_class": "TextToolParameter", "hidden": false, "refresh_on_change": false, "type": "text", "name": "suffix_pattern" } ] }, { "model_class": "ConditionalWhen", "value": "suffix_every", "inputs": [ { "default_value": "_#", "help": "Describe the suffix pattern to use when joing element name and data copy number. For instance, the default is '_#', which will produce _1 as the first suffix used.", "area": false, "datalist": [], "text_value": "_#", "argument": null, "value": "_#", "label": "Use the follow suffix pattern:", "is_dynamic": false, "optional": false, "model_class": "TextToolParameter", "hidden": false, "refresh_on_change": false, "type": "text", "name": "suffix_pattern" } ] }, { "model_class": "ConditionalWhen", "value": "keep_first", "inputs": [] }, { "model_class": "ConditionalWhen", "value": "keep_last", "inputs": [] }, { "model_class": "ConditionalWhen", "value": "fail", "inputs": [] } ], "type": "conditional", "name": "conflict" } ], "help": null, "title": "Advanced Options", "expanded": false, "model_class": "Section", "type": "section", "name": "advanced" } ], "xrefs": [], "description": "into single list of datasets", "warnings": "", "replacement_parameters": [], "history_id": "8f7a155755f10e73", "panel_section_name": "Collection Operations", "edam_topics": [], "tool_errors": null, "enctype": "application/x-www-form-urlencoded", "name": "Merge Collections", "versions": [ "1.0.0" ], "message": "", "step_type": "tool", "edam_operations": [], "method": "post", "step_name": "Merge Collections", "action": "/tool_runner/index", "model_class": "MergeCollectionTool", "display": true }, { "help": "

WARNING: Be careful not to concatenate datasets of different kinds (e.g., sequences with intervals). This tool does not check if the datasets being concatenated are in the same format.

\n
\n

What it does

\n

Concatenates datasets

\n
\n

Example

\n

Concatenating Dataset:

\n
\nchrX  151087187  151087355  A  0  -\nchrX  151572400  151572481  B  0  +\n
\n

with Dataset1:

\n
\nchr1  151242630  151242955  X  0  +\nchr1  151271715  151271999  Y  0  +\nchr1  151278832  151279227  Z  0  -\n
\n

and with Dataset2:

\n
\nchr2  100000030  200000955  P  0  +\nchr2  100000015  200000999  Q  0  +\n
\n

will result in the following:

\n
\nchrX  151087187  151087355  A  0  -\nchrX  151572400  151572481  B  0  +\nchr1  151242630  151242955  X  0  +\nchr1  151271715  151271999  Y  0  +\nchr1  151278832  151279227  Z  0  -\nchr2  100000030  200000955  P  0  +\nchr2  100000015  200000999  Q  0  +\n
\n
\n

Citation

\n

If you use this tool in Galaxy, please cite:

\n

Bjoern A. Gruening (2014), Galaxy wrapper

\n

Assaf Gordon (gordon <at> cshl dot edu)

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What it does

\n

This tool selects N random lines from a file, with no repeats, and preserving ordering.

\n
\n

Example

\n

Input File:

\n
\nchr7  56632  56652   D17003_CTCF_R6  310  +\nchr7  56736  56756   D17003_CTCF_R7  354  +\nchr7  56761  56781   D17003_CTCF_R4  220  +\nchr7  56772  56792   D17003_CTCF_R7  372  +\nchr7  56775  56795   D17003_CTCF_R4  207  +\n
\n

Selecting 2 random lines might return this:

\n
\nchr7  56736  56756   D17003_CTCF_R7  354  +\nchr7  56775  56795   D17003_CTCF_R4  207  +\n
\n", "labels": [], "panel_section_id": "text_manipulation", "sharable_url": null, "id": "random_lines1", "step_label": "", "job_remap": false, "errors": {}, "requirements": [], "job_id": null, "citations": false, "post_job_actions": [], "form_style": "regular", "output_connections": [], "step_index": 3, "version": "2.0.2", "state_inputs": { "input": "{\"__class__\": \"ConnectedValue\"}", "seed_source": "{\"__current_case__\": 1, \"seed\": \"${wf_param}\", \"seed_source_selector\": \"set_seed\"}", "num_lines": "{\"__class__\": \"RuntimeValue\"}" }, "step_version": "2.0.2", "inputs": [ { "default_value": "1", "help": "lines", "area": false, "datalist": [], "max": null, "min": null, "argument": null, "value": { "__class__": "RuntimeValue" }, "label": "Randomly select", "is_dynamic": false, "optional": false, "text_value": "Not available.", "model_class": "IntegerToolParameter", "hidden": false, "refresh_on_change": false, "type": "integer", "name": "num_lines" }, { "default_value": { "values": [ { "src": "hda", "id": "bbd44e69cb8906b50467c46e02ff909c" } ] }, "multiple": false, "help": "", "text_value": "Not available.", "optional": false, "argument": null, "value": { "__class__": "ConnectedValue" }, "label": "from", "is_dynamic": false, "extensions": [ "txt" ], "edam": { "edam_data": [ "data_0006" ], "edam_formats": [ "format_2330" ] }, "model_class": "DataToolParameter", "hidden": false, "refresh_on_change": true, "type": "data", "options": { "hdca": [], "hda": [ { "src": "hda", "name": "SRR5363633_1.fastq.gz (as fqtoc)", "tags": [], "keep": false, "hid": 1, "id": "bbd44e69cb8906b50467c46e02ff909c" } ] }, "name": "input" }, { "test_param": { "multiple": false, "help": "", "display": null, "text_value": "Set seed", "argument": null, "value": "set_seed", "label": "Set a random seed", "is_dynamic": false, "optional": false, "textable": true, "model_class": "SelectToolParameter", "hidden": false, "refresh_on_change": true, "type": "select", "options": [ [ "Don't set seed", "no_seed", true ], [ "Set seed", "set_seed", false ] ], "name": "seed_source_selector" }, "model_class": "Conditional", "cases": [ { "model_class": "ConditionalWhen", "value": "no_seed", "inputs": [] }, { "model_class": "ConditionalWhen", "value": "set_seed", "inputs": [ { "default_value": "", "help": "", "area": false, "datalist": [], "text_value": "${wf_param}", "argument": null, "value": "${wf_param}", "label": "Random seed", "is_dynamic": false, "optional": false, "model_class": "TextToolParameter", "hidden": false, "refresh_on_change": false, "type": "text", "name": "seed" } ] } ], "type": "conditional", "name": "seed_source" } ], "xrefs": [], "description": "from a file", "warnings": "", "replacement_parameters": [], "history_id": "8f7a155755f10e73", "panel_section_name": "Text Manipulation", "edam_topics": [], "tool_errors": null, "enctype": "application/x-www-form-urlencoded", "name": "Select random lines", "versions": [ "2.0.2" ], "message": "", "step_type": "tool", "edam_operations": [], "method": "post", "step_name": "Select random lines", "action": "/tool_runner/index", "model_class": "Tool", "display": true }, { "inputs":[ { "area":false, "argument":null, "datalist":[], "help":null, "hidden":false, "is_dynamic":false, "label":"", "model_class":"TextToolParameter", "name":"input", "optional":false, "refresh_on_change":false, "type":"text", "value":null } ], "output_connections":[], "replacement_parameters":[], "step_index":4, "step_label":"", "step_name":"Input parameter", "step_type":"parameter_input", "step_version":null } ], "has_upgrade_messages": false, "id": "ebab00128497f9d7", "workflow_resource_parameters": null }