Mercurial > repos > stemcellcommons > ngs_peak_calling_workflows
view MACS2_SPP_ChIP-Seq.ga @ 0:8d4be9af8a51 draft default tip
Uploaded
author | stemcellcommons |
---|---|
date | Tue, 28 Jan 2014 11:30:42 -0500 |
parents | |
children |
line wrap: on
line source
{ "a_galaxy_workflow": "true", "annotation": "{\"refinery_type\": \"analysis\", \"refinery_relationships\": [{\"category\": \"1-1\", \"set1\": \"input_file\", \"set2\": \"exp_file\"}]}", "format-version": "0.1", "name": "MACS2+SPP ChIP-Seq = groomer + bowtie + filter + cut + igvtools", "steps": { "0": { "annotation": "", "id": 0, "input_connections": {}, "inputs": [ { "description": "", "name": "exp_file" } ], "name": "Input dataset", "outputs": [], "position": { "left": 299.75, "top": 300.140625 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"exp_file\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "1": { "annotation": "", "id": 1, "input_connections": {}, "inputs": [ { "description": "", "name": "input_file" } ], "name": "Input dataset", "outputs": [], "position": { "left": 299.75, "top": 491.140625 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"input_file\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "2": { "annotation": "", "id": 2, "input_connections": { "input_file": { "id": 0, "output_name": "output" } }, "inputs": [], "name": "FASTQ Parallel Groomer", "outputs": [ { "name": "output_file", "type": "fastqsanger" } ], "position": { "left": 500.4375, "top": 299.328125 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"options_type_selector\\\": \\\"advanced\\\", \\\"__current_case__\\\": 1, \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"null\"}", "tool_version": "0.3.1", "type": "tool", "user_outputs": [] }, "3": { "annotation": "", "id": 3, "input_connections": { "input_file": { "id": 1, "output_name": "output" } }, "inputs": [], "name": "FASTQ Parallel Groomer", "outputs": [ { "name": "output_file", "type": "fastqsanger" } ], "position": { "left": 499.5, "top": 490 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"options_type_selector\\\": \\\"advanced\\\", \\\"__current_case__\\\": 1, \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"null\"}", "tool_version": "0.3.1", "type": "tool", "user_outputs": [] }, "4": { "annotation": "", "id": 4, "input_connections": { "singlePaired|sInput1": { "id": 2, "output_name": "output_file" } }, "inputs": [], "name": "Map with Bowtie for Illumina", "outputs": [ { "name": "output", "type": "sam" }, { "name": "output_suppressed_reads_l", "type": "fastq" }, { "name": "output_suppressed_reads_r", "type": "fastq" }, { "name": "output_unmapped_reads_l", "type": "fastq" }, { "name": "output_unmapped_reads_r", "type": "fastq" } ], "position": { "left": 799.75, "top": 299.140625 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.2", "tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"dm3\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": null, \\\"sParams\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sUnmappedFile\\\": \\\"False\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSeed\\\": \\\"-1\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sMaqSoapAlign\\\": \\\"-1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sTryHard\\\": \\\"noTryHard\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sdStrata\\\": \\\"noStrata\\\", \\\"sdMaxBacktracks\\\": \\\"800\\\", \\\"sBest\\\": \\\"doBest\\\", \\\"__current_case__\\\": 1}, \\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeedLen\\\": \\\"28\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"sMaxFile\\\": \\\"False\\\"}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", "tool_version": "1.1.2", "type": "tool", "user_outputs": [] }, "5": { "annotation": "", "id": 5, "input_connections": { "singlePaired|sInput1": { "id": 3, "output_name": "output_file" } }, "inputs": [], "name": "Map with Bowtie for Illumina", "outputs": [ { "name": "output", "type": "sam" }, { "name": "output_suppressed_reads_l", "type": "fastq" }, { "name": "output_suppressed_reads_r", "type": "fastq" }, { "name": "output_unmapped_reads_l", "type": "fastq" }, { "name": "output_unmapped_reads_r", "type": "fastq" } ], "position": { "left": 800.75, "top": 493.140625 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.2", "tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"dm3\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": null, \\\"sParams\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sUnmappedFile\\\": \\\"False\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSeed\\\": \\\"-1\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sMaqSoapAlign\\\": \\\"-1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sTryHard\\\": \\\"noTryHard\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sdStrata\\\": \\\"noStrata\\\", \\\"sdMaxBacktracks\\\": \\\"800\\\", \\\"sBest\\\": \\\"doBest\\\", \\\"__current_case__\\\": 1}, \\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeedLen\\\": \\\"28\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"sMaxFile\\\": \\\"False\\\"}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", "tool_version": "1.1.2", "type": "tool", "user_outputs": [] }, "6": { "annotation": "", "id": 6, "input_connections": { "source|input1": { "id": 4, "output_name": "output" } }, "inputs": [], "name": "SAM-to-BAM", "outputs": [ { "name": "output1", "type": "bam" } ], "position": { "left": 1142.25, "top": 326.640625 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "sam_to_bam", "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", "tool_version": "1.1.2", "type": "tool", "user_outputs": [] }, "7": { "annotation": "", "id": 7, "input_connections": { "source|input1": { "id": 5, "output_name": "output" } }, "inputs": [], "name": "SAM-to-BAM", "outputs": [ { "name": "output1", "type": "bam" } ], "position": { "left": 1135.25, "top": 520.125 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "sam_to_bam", "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", "tool_version": "1.1.2", "type": "tool", "user_outputs": [] }, "8": { "annotation": "{\"output_tdf\": {\"name\": \"igv_count_1\", \"description\": \"\", \"type\": \"tdf\"}}", "id": 8, "input_connections": { "input": { "id": 6, "output_name": "output1" } }, "inputs": [], "name": "IGVtools count", "outputs": [ { "name": "output_tdf", "type": "igv.tdf" }, { "name": "output_wig", "type": "wig" } ], "position": { "left": 1575.75, "top": 220.140625 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_count/1.0", "tool_state": "{\"__page__\": 0, \"extend\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"zoom\": \"\\\"7\\\"\", \"window\": \"\\\"25\\\"\", \"output_fmt\": \"\\\"output.tdf\\\"\", \"input\": \"null\", \"refGenomeSource\": \"{\\\"refGenomeSource_type\\\": \\\"built-in\\\", \\\"ref\\\": \\\"/n/hsphS10/hsphfs1/chb/biodata/genomes/igv/dm3.genome\\\", \\\"__current_case__\\\": 0}\", \"window_functions\": \"\\\"mean\\\"\"}", "tool_version": "1.0", "type": "tool", "user_outputs": [] }, "9": { "annotation": "", "id": 9, "input_connections": { "major_command|input_chipseq_file1": { "id": 6, "output_name": "output1" }, "major_command|input_control_file1": { "id": 7, "output_name": "output1" } }, "inputs": [], "name": "SPP", "outputs": [ { "name": "output_default_file", "type": "txt" }, { "name": "output_narrow_peak", "type": "txt" }, { "name": "output_plot_file", "type": "pdf" }, { "name": "output_region_peak", "type": "txt" }, { "name": "output_peakshift_file", "type": "txt" }, { "name": "output_rdata_file", "type": "txt" } ], "position": { "left": 1573, "top": 365 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/stemcellcommons/spp_tool/spp_peak_calling/1.11.0", "tool_state": "{\"major_command\": \"{\\\"save_plot_file\\\": \\\"True\\\", \\\"input_chipseq_file1\\\": null, \\\"replace\\\": \\\"True\\\", \\\"num_peaks\\\": \\\"0\\\", \\\"major_command_selector\\\": \\\"peak_calling\\\", \\\"save_rdata_file\\\": \\\"False\\\", \\\"input_control_file1\\\": null, \\\"__current_case__\\\": 1, \\\"save_regionpeak_file\\\": \\\"True\\\", \\\"save_narrowpeak_file\\\": \\\"True\\\", \\\"fdr\\\": \\\"0.1\\\"}\", \"__page__\": 0, \"experiment_name\": \"\\\"SPP in Galaxy\\\"\", \"__rerun_remap_job_id__\": null}", "tool_version": "1.11.0", "type": "tool", "user_outputs": [] }, "10": { "annotation": "{\"output_tdf\": {\"name\": \"igv_count_2\", \"description\": \"\", \"type\": \"tdf\"}}", "id": 10, "input_connections": { "input": { "id": 7, "output_name": "output1" } }, "inputs": [], "name": "IGVtools count", "outputs": [ { "name": "output_tdf", "type": "igv.tdf" }, { "name": "output_wig", "type": "wig" } ], "position": { "left": 1575.75, "top": 642.140625 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_count/1.0", "tool_state": "{\"__page__\": 0, \"extend\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"zoom\": \"\\\"7\\\"\", \"window\": \"\\\"25\\\"\", \"output_fmt\": \"\\\"output.tdf\\\"\", \"input\": \"null\", \"refGenomeSource\": \"{\\\"refGenomeSource_type\\\": \\\"built-in\\\", \\\"ref\\\": \\\"/n/hsphS10/hsphfs1/chb/biodata/genomes/igv/danRer7.genome\\\", \\\"__current_case__\\\": 0}\", \"window_functions\": \"\\\"mean\\\"\"}", "tool_version": "1.0", "type": "tool", "user_outputs": [] }, "11": { "annotation": "", "id": 11, "input_connections": { "major_command|input_chipseq_file1": { "id": 6, "output_name": "output1" }, "major_command|input_control_file1": { "id": 7, "output_name": "output1" } }, "inputs": [], "name": "MACS2", "outputs": [ { "name": "output_bed_file", "type": "bed" }, { "name": "output_extra_files", "type": "html" }, { "name": "output_peaks_file", "type": "xls" }, { "name": "output_narrowpeaks_file", "type": "txt" }, { "name": "output_xls_to_interval_peaks_file", "type": "interval" }, { "name": "output_xls_to_interval_negative_peaks_file", "type": "interval" }, { "name": "output_bdgcmp_file", "type": "bdg" } ], "position": { "left": 1574, "top": 786 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/stemcellcommons/macs2/macs2_peakcalling/2.0.10", "tool_state": "{\"major_command\": \"{\\\"gsize\\\": \\\"1400000000.0\\\", \\\"bdg\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"advanced_options\\\": {\\\"mfoldlo\\\": \\\"10\\\", \\\"nolambda\\\": \\\"False\\\", \\\"advanced_options_selector\\\": \\\"on\\\", \\\"mfoldhi\\\": \\\"30\\\", \\\"__current_case__\\\": 0}, \\\"input_chipseq_file1\\\": null, \\\"xls_to_interval\\\": \\\"False\\\", \\\"major_command_selector\\\": \\\"callpeak\\\", \\\"input_control_file1\\\": null, \\\"pq_options\\\": {\\\"pq_options_selector\\\": \\\"qvalue\\\", \\\"qvalue\\\": \\\"0.05\\\", \\\"__current_case__\\\": 1}, \\\"bw\\\": \\\"200\\\", \\\"nomodel_type\\\": {\\\"nomodel_type_selector\\\": \\\"create_model\\\", \\\"__current_case__\\\": 1}}\", \"__page__\": 0, \"experiment_name\": \"\\\"MACS2 in Galaxy\\\"\", \"__rerun_remap_job_id__\": null}", "tool_version": "2.0.10", "type": "tool", "user_outputs": [] }, "12": { "annotation": "", "id": 12, "input_connections": { "input": { "id": 9, "output_name": "output_narrow_peak" } }, "inputs": [], "name": "Cut", "outputs": [ { "name": "out_file1", "type": "tabular" } ], "position": { "left": 1818.75, "top": 321.140625 }, "post_job_actions": { "ChangeDatatypeActionout_file1": { "action_arguments": { "newtype": "bed" }, "action_type": "ChangeDatatypeAction", "output_name": "out_file1" } }, "tool_errors": null, "tool_id": "Cut1", "tool_state": "{\"columnList\": \"\\\"c1,c2,c3,c4,c7\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", "tool_version": "1.0.2", "type": "tool", "user_outputs": [] }, "13": { "annotation": "", "id": 13, "input_connections": { "input": { "id": 9, "output_name": "output_region_peak" } }, "inputs": [], "name": "Cut", "outputs": [ { "name": "out_file1", "type": "tabular" } ], "position": { "left": 1810.734375, "top": 554.125 }, "post_job_actions": { "ChangeDatatypeActionout_file1": { "action_arguments": { "newtype": "bed" }, "action_type": "ChangeDatatypeAction", "output_name": "out_file1" } }, "tool_errors": null, "tool_id": "Cut1", "tool_state": "{\"columnList\": \"\\\"c1,c2,c3,c4,c7\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", "tool_version": "1.0.2", "type": "tool", "user_outputs": [] }, "14": { "annotation": "", "id": 14, "input_connections": { "input": { "id": 11, "output_name": "output_bed_file" } }, "inputs": [], "name": "IGVtools sort", "outputs": [ { "name": "output_sam", "type": "sam" }, { "name": "output_bed", "type": "sam" }, { "name": "output_vcf", "type": "sam" }, { "name": "output_psl", "type": "sam" }, { "name": "output_igv", "type": "sam" }, { "name": "output_cn", "type": "sam" } ], "position": { "left": 2023.9375, "top": 880.9375 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_sort/1.0", "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", "tool_version": "1.0", "type": "tool", "user_outputs": [] }, "15": { "annotation": "{\"out_file1\": {\"name\": \"spp_filtered_narrowpeak\", \"description\": \"\", \"type\": \"txt\"}}", "id": 15, "input_connections": { "input": { "id": 12, "output_name": "out_file1" } }, "inputs": [], "name": "Filter", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 1838.1875, "top": 440.8125 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "Filter1", "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c5>15\\\"\", \"__page__\": 0}", "tool_version": "1.1.0", "type": "tool", "user_outputs": [] }, "16": { "annotation": "{\"out_file1\": {\"name\": \"spp_filtered_regionpeak\", \"description\": \"\", \"type\": \"txt\"}}", "id": 16, "input_connections": { "input": { "id": 13, "output_name": "out_file1" } }, "inputs": [], "name": "Filter", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 1818.25, "top": 663.859375 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "Filter1", "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c5>15\\\"\", \"__page__\": 0}", "tool_version": "1.1.0", "type": "tool", "user_outputs": [] }, "17": { "annotation": "{\"output_tdf\": {\"name\": \"igv_count_5\", \"description\": \"\", \"type\": \"tdf\"}}", "id": 17, "input_connections": { "input": { "id": 14, "output_name": "output_bed" } }, "inputs": [], "name": "IGVtools count", "outputs": [ { "name": "output_tdf", "type": "igv.tdf" }, { "name": "output_wig", "type": "wig" } ], "position": { "left": 2358.265625, "top": 882.09375 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_count/1.0", "tool_state": "{\"__page__\": 0, \"extend\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"zoom\": \"\\\"7\\\"\", \"window\": \"\\\"25\\\"\", \"output_fmt\": \"\\\"output.tdf\\\"\", \"input\": \"null\", \"refGenomeSource\": \"{\\\"refGenomeSource_type\\\": \\\"built-in\\\", \\\"ref\\\": \\\"/n/hsphS10/hsphfs1/chb/biodata/genomes/igv/dm3.genome\\\", \\\"__current_case__\\\": 0}\", \"window_functions\": \"\\\"mean\\\"\"}", "tool_version": "1.0", "type": "tool", "user_outputs": [] }, "18": { "annotation": "", "id": 18, "input_connections": { "input": { "id": 15, "output_name": "out_file1" } }, "inputs": [], "name": "IGVtools sort", "outputs": [ { "name": "output_sam", "type": "sam" }, { "name": "output_bed", "type": "sam" }, { "name": "output_vcf", "type": "sam" }, { "name": "output_psl", "type": "sam" }, { "name": "output_igv", "type": "sam" }, { "name": "output_cn", "type": "sam" } ], "position": { "left": 2026.75, "top": 231.140625 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_sort/1.0", "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", "tool_version": "1.0", "type": "tool", "user_outputs": [] }, "19": { "annotation": "", "id": 19, "input_connections": { "input": { "id": 16, "output_name": "out_file1" } }, "inputs": [], "name": "IGVtools sort", "outputs": [ { "name": "output_sam", "type": "sam" }, { "name": "output_bed", "type": "sam" }, { "name": "output_vcf", "type": "sam" }, { "name": "output_psl", "type": "sam" }, { "name": "output_igv", "type": "sam" }, { "name": "output_cn", "type": "sam" } ], "position": { "left": 2021.75, "top": 554.140625 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_sort/1.0", "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", "tool_version": "1.0", "type": "tool", "user_outputs": [] }, "20": { "annotation": "{\"output_tdf\": {\"name\": \"igv_count_3\", \"description\": \"\", \"type\": \"tdf\"}}", "id": 20, "input_connections": { "input": { "id": 18, "output_name": "output_bed" } }, "inputs": [], "name": "IGVtools count", "outputs": [ { "name": "output_tdf", "type": "igv.tdf" }, { "name": "output_wig", "type": "wig" } ], "position": { "left": 2338.75, "top": 337.140625 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_count/1.0", "tool_state": "{\"__page__\": 0, \"extend\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"zoom\": \"\\\"7\\\"\", \"window\": \"\\\"25\\\"\", \"output_fmt\": \"\\\"output.tdf\\\"\", \"input\": \"null\", \"refGenomeSource\": \"{\\\"refGenomeSource_type\\\": \\\"built-in\\\", \\\"ref\\\": \\\"/n/hsphS10/hsphfs1/chb/biodata/genomes/igv/dm3.genome\\\", \\\"__current_case__\\\": 0}\", \"window_functions\": \"\\\"mean\\\"\"}", "tool_version": "1.0", "type": "tool", "user_outputs": [] }, "21": { "annotation": "{\"output_tdf\": {\"name\": \"igv_count_4\", \"description\": \"\", \"type\": \"tdf\"}}", "id": 21, "input_connections": { "input": { "id": 19, "output_name": "output_bed" } }, "inputs": [], "name": "IGVtools count", "outputs": [ { "name": "output_tdf", "type": "igv.tdf" }, { "name": "output_wig", "type": "wig" } ], "position": { "left": 2345.75, "top": 567.140625 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_count/1.0", "tool_state": "{\"__page__\": 0, \"extend\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"zoom\": \"\\\"7\\\"\", \"window\": \"\\\"25\\\"\", \"output_fmt\": \"\\\"output.tdf\\\"\", \"input\": \"null\", \"refGenomeSource\": \"{\\\"refGenomeSource_type\\\": \\\"built-in\\\", \\\"ref\\\": \\\"/n/hsphS10/hsphfs1/chb/biodata/genomes/igv/dm3.genome\\\", \\\"__current_case__\\\": 0}\", \"window_functions\": \"\\\"mean\\\"\"}", "tool_version": "1.0", "type": "tool", "user_outputs": [] } } }