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Changeset 10:2c8931827fa5 (2015-03-30)

Previous changeset 9:3b5eecc9551e (2013-10-25) Next changeset 11:99209ed2ec87 (2017-02-01)

Commit message:
Uploaded with note about NR versioning

modified:
README.rst
repository_dependencies.xml

added:
N_abberans_piechart_mouseover.png
blast_top_hit_species.ga
blast_top_hit_species.png

removed:
secreted_protein_workflow.ga

diff -r 3b5eecc9551e -r 2c8931827fa5 N_abberans_piechart_mouseover.png

Binary file N_abberans_piechart_mouseover.png has changed

diff -r 3b5eecc9551e -r 2c8931827fa5 README.rst
--- a/README.rst Fri Oct 25 10:22:35 2013 -0400
+++ b/README.rst Mon Mar 30 11:46:13 2015 -0400

b"@@ -1,99 +1,180 @@\n-This is package is a Galaxy workflow for the identification of candidate\n-secreted proteins from a given protein FASTA file.\n+Introduction\n+============\n+\n+Galaxy is a web-based platform for biological data analysis, supporting\n+extension with additional tools (often wrappers for existing command line\n+tools) and datatypes. See http://www.galaxyproject.org/ and the public\n+server at http://usegalaxy.org for an example.\n+\n+The NCBI BLAST suite is a widely used set of tools for biological sequence\n+comparison. It is available as standalone binaries for use at the command\n+line, and via the NCBI website for smaller searches. For more details see\n+http://blast.ncbi.nlm.nih.gov/Blast.cgi\n+\n+This is an example workflow using the Galaxy wrappers for NCBI BLAST+,\n+see https://github.com/peterjc/galaxy_blast\n+\n+\n+Galaxy workflow for counting species of top BLAST hits \n+======================================================\n+\n+This Galaxy workflow (file ``blast_top_hit_species.ga``) is intended for an\n+initial assessment of a transcriptome assembly to give a crude indication of\n+any major contamination present based on the species of the top BLAST hit\n+of 1000 representative sequences.\n+\n+.. image:: https://raw.githubusercontent.com/peterjc/galaxy_blast/master/workflows/blast_top_hit_species/blast_top_hit_species.png\n+\n+In words, the workflow proceeds as follows:\n+\n+1. Upload/import your transcriptome assembly or any nucleotide FASTA file.\n+2. Samples 1000 representative sequences, selected uniformly/evenly though\n+ the file.\n+3. Convert the sampled FASTA file into a three column tabular file.\n+4. Runs NCBI BLASTX of the sampled FASTA file against the latest NCBI ``nr``\n+ database (assuming this is already available setup on your local Galaxy\n+ under the alias ``nr``), requesting tabular output including the taxonomy\n+ fields, and at most one matching target sequence.\n+5. Remove any duplicate alignments (multiple HSPs for the same match).\n+6. Combine the filtered BLAST output with the tabular version of the 1000\n+ sequences to give a new tabular file with exactly 1000 lines, adding\n+ ``None`` for sequences missing a BLAST hit.\n+7. Count the BLAST species names in this file.\n+8. Sort the counts.\n+\n+Finally we would suggest visualising the sorted tally table as a Pie Chart.\n+\n+\n+Sample Data\n+===========\n+\n+As an example, you can upload the transcriptome assembly of the nematode\n+*Nacobbus abberans* from Eves van den Akker *et al.* (2015),\n+http://dx.doi.org/10.1093/gbe/evu171 using this URL:\n+\n+http://nematode.net/Data/nacobbus_aberrans_transcript_assembly/N.abberans_reference_no_contam.zip\n+\n+Running this workflow with a copy of the NCBI non-redundant ``nr`` database\n+from 16 Oct 2014 (which did **not** contain this *N. abberans* dataset) gave\n+the following results - note 609 out of the 1000 sequences gave no BLAST hit.\n \n-It runs SignalP v3.0 (Bendtsen et al. 2004) and selects only proteins with a\n-strong predicted signal peptide, and then runs TMHMM v2.0 (Krogh et al. 2001)\n-on those, and selects only proteins without a predicted trans-membrane helix.\n-This workflow was used in Kikuchi et al. (2011), and is a simplification of\n-the candidate effector protocol described in Jones et al. (2009).\n+===== ==================\n+Count Subject Blast Name\n+----- ------------------\n+ 609 None\n+ 244 nematodes\n+ 30 ascomycetes\n+ 27 eukaryotes\n+ 8 basidiomycetes\n+ 6 aphids\n+ 5 eudicots\n+ 5 flies\n+ ... ...\n+===== ==================\n+\n+As you might guess from\tthe filename ``N.abberans_reference_no_contam.fasta``,\n+this transcriptome assembly has already had obvious contamination removed.\n+\n+At the time of writing, Galaxy's visualizations could not be included in\n+a workflow. You can generate a pie chart from the final count file using\n+the counts (c1) and labels (c2), like this:\n+\n+.. image:: https://raw.githubusercontent.com/peterjc/galaxy_blast/master/workflows/blast_top_hit_species/N_abberans_piech"..b'sm in the emerging plant\n-pathogen *Bursaphelenchus xylophilus*. PLoS Pathog 7: e1002219.\n-http://dx.doi.org/10.1371/journal.ppat.1002219\n+Automated Installation\n+======================\n \n-Jones, J.T., Kumar, A., Pylypenko, L.A., Thirugnanasambandam, A., et al. (2009)\n-Identification and functional characterization of effectors in expressed\n-sequence tags from various life cycle stages of the potato cyst nematode\n-*Globodera pallida*. Mol Plant Pathol 10: 815\xe2\x80\x9328.\n-http://dx.doi.org/10.1111/j.1364-3703.2009.00585.x\n-\n+Installation via the Galaxy Tool Shed should take care of the dependencies\n+on Galaxy tools including the NCBI BLAST+ wrappers and associated binaries.\n \n-Dependencies\n-============\n-\n-These dependencies should be resolved automatically via the Galaxy Tool Shed:\n-\n-* http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp\n-* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id\n-\n-However, at the time of writing those Galaxy tools have their own\n-dependencies required for this workflow which require manual\n-installation (SignalP v3.0 and TMHMM v2.0).\n+However, this workflow requires a current version of the NCBI nr protein\n+BLAST database to be listed in ``blastdb_p.loc`` with the key ``nr`` (lower\n+case).\n \n \n History\n@@ -102,12 +183,7 @@\n ======= ======================================================================\n Version Changes\n ------- ----------------------------------------------------------------------\n-v0.0.1 - Initial release to Tool Shed (May, 2013)\n- - Expanded README file to include example data\n-v0.0.2 - Updated versions of the tools used, inclulding core Galaxy Filter\n- tool to avoid warning about new ``header_lines`` parameter.\n- - Added link to Tool Shed in the workflow annotation explaining there\n- is a README file with sample data, and a requested citation.\n+v0.1.0 - Initial Tool Shed release, targetting NCBI BLAST+ 2.2.29\n ======= ======================================================================\n \n \n@@ -116,15 +192,39 @@\n \n This workflow is under source code control here:\n \n-https://github.com/peterjc/pico_galaxy/tree/master/workflows/secreted_protein_workflow\n+https://github.com/peterjc/galaxy_blast/tree/master/workflows/blast_top_hit_species\n \n To prepare the tar-ball for uploading to the Tool Shed, I use this:\n \n- $ tar -cf secreted_protein_workflow.tar.gz README.rst repository_dependencies.xml secreted_protein_workflow.ga\n+ $ tar -cf blast_top_hit_species.tar.gz README.rst repository_dependencies.xml blast_top_hit_species.ga blast_top_hit_species.png N_abberans_piechart_mouseover.png\n \n Check this,\n \n- $ tar -tzf secreted_protein_workflow.tar.gz \n+ $ tar -tzf blast_top_hit_species.tar.gz\n README.rst\n repository_dependencies.xml\n- secreted_protein_workflow.ga\n+ blast_top_hit_species.ga\n+ blast_top_hit_species.png\n+ N_abberans_piechart_mouseover.png\n+\n+\n+Licence (MIT)\n+=============\n+\n+Permission is hereby granted, free of charge, to any person obtaining a copy\n+of this software and associated documentation files (the "Software"), to deal\n+in the Software without restriction, including without limitation the rights\n+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n+copies of the Software, and to permit persons to whom the Software is\n+furnished to do so, subject to the following conditions:\n+\n+The above copyright notice and this permission notice shall be included in\n+all copies or substantial portions of the Software.\n+\n+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n+THE SOFTWARE.\n'

diff -r 3b5eecc9551e -r 2c8931827fa5 blast_top_hit_species.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/blast_top_hit_species.ga Mon Mar 30 11:46:13 2015 -0400

[

b'@@ -0,0 +1,331 @@\n+{\n+ "a_galaxy_workflow": "true", \n+ "annotation": "", \n+ "format-version": "0.1", \n+ "name": "Species of top BLAST hits", \n+ "steps": {\n+ "0": {\n+ "annotation": "", \n+ "id": 0, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Transcriptome FASTA file"\n+ }\n+ ], \n+ "label": null, \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 242, \n+ "top": 119\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Transcriptome FASTA file\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "user_outputs": [], \n+ "uuid": "e445b44b-02a7-4fd1-8944-cd680f967062"\n+ }, \n+ "1": {\n+ "annotation": "This workflow is deliberately a simple/crude assessment, and there is no need to run BLASTX on all the sequences - a sample of 1000 should be enough.", \n+ "id": 1, \n+ "input_connections": {\n+ "input_file": {\n+ "id": 0, \n+ "output_name": "output"\n+ }\n+ }, \n+ "inputs": [], \n+ "label": null, \n+ "name": "Sub-sample sequences files", \n+ "outputs": [\n+ {\n+ "name": "output_file", \n+ "type": "input"\n+ }\n+ ], \n+ "position": {\n+ "left": 435, \n+ "top": 119\n+ }, \n+ "post_job_actions": {\n+ "RenameDatasetActionoutput_file": {\n+ "action_arguments": {\n+ "newname": "1000 sequences from #{input_file}"\n+ }, \n+ "action_type": "RenameDatasetAction", \n+ "output_name": "output_file"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/0.2.1", \n+ "tool_state": "{\\"__page__\\": 0, \\"input_file\\": \\"null\\", \\"__rerun_remap_job_id__\\": null, \\"sampling\\": \\"{\\\\\\"count\\\\\\": \\\\\\"1000\\\\\\", \\\\\\"type\\\\\\": \\\\\\"desired_count\\\\\\", \\\\\\"__current_case__\\\\\\": 2}\\", \\"chromInfo\\": \\"\\\\\\"/mnt/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"interleaved\\": \\"\\\\\\"False\\\\\\"\\"}", \n+ "tool_version": "0.2.1", \n+ "type": "tool", \n+ "user_outputs": [], \n+ "uuid": "87ce69ef-5fb0-41b0-9575-d3b96544f8be"\n+ }, \n+ "2": {\n+ "annotation": "We only want one line per query, so limit this to the best scoring target sequence. Assumes current NCBI nr database is available locally as \\"nr\\".", \n+ "id": 2, \n+ "input_connections": {\n+ "query": {\n+ "id": 1, \n+ "output_name": "output_file"\n+ }\n+ }, \n+ "inputs": [], \n+ "label": null, \n+ "name": "NCBI BLAST+ blastx", \n+ "outputs": [\n+ {\n+ "name": "output1", \n+ "type": "tabular"\n+ }\n+ ], \n+ "position": {\n+ "left": 489, \n+ "top": 263\n+ }, \n+ "post_job_actions": {\n+ "RenameDatasetActionoutput1": {\n+ "action_arguments": {\n+ "newname": "Top BLAST match"\n+ }, \n+ "action_type": "RenameDatasetAction", \n+ "output_name": "output1"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_pl'..b'lue\\\\\\": \\\\\\"None\\\\\\", \\\\\\"__current_case__\\\\\\": 0}, \\\\\\"fill_columns_by\\\\\\": \\\\\\"fill_unjoined_only\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"unmatched\\": \\"\\\\\\"-u\\\\\\"\\", \\"input1\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/mnt/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\"}", \n+ "tool_version": "2.0.2", \n+ "type": "tool", \n+ "user_outputs": [], \n+ "uuid": "4c280b0e-b4a6-4ae4-8a81-d6e93932ef71"\n+ }, \n+ "6": {\n+ "annotation": "Here we make a tally table of the BLAST species name column", \n+ "id": 6, \n+ "input_connections": {\n+ "input": {\n+ "id": 5, \n+ "output_name": "out_file1"\n+ }\n+ }, \n+ "inputs": [], \n+ "label": null, \n+ "name": "Count", \n+ "outputs": [\n+ {\n+ "name": "out_file1", \n+ "type": "tabular"\n+ }\n+ ], \n+ "position": {\n+ "left": 952, \n+ "top": 398\n+ }, \n+ "post_job_actions": {\n+ "HideDatasetActionout_file1": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "out_file1"\n+ }, \n+ "RenameDatasetActionout_file1": {\n+ "action_arguments": {\n+ "newname": "Top BLAST hit species counts (unsorted)"\n+ }, \n+ "action_type": "RenameDatasetAction", \n+ "output_name": "out_file1"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "Count1", \n+ "tool_state": "{\\"__page__\\": 0, \\"column\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": [\\\\\\"19\\\\\\"]}\\", \\"__rerun_remap_job_id__\\": null, \\"delim\\": \\"\\\\\\"T\\\\\\"\\", \\"input\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/mnt/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\"}", \n+ "tool_version": "1.0.0", \n+ "type": "tool", \n+ "user_outputs": [], \n+ "uuid": "d3322137-1911-426d-87a7-c82b5fc16825"\n+ }, \n+ "7": {\n+ "annotation": "Sorting the counts makes the results easier to interpret directly.", \n+ "id": 7, \n+ "input_connections": {\n+ "input": {\n+ "id": 6, \n+ "output_name": "out_file1"\n+ }\n+ }, \n+ "inputs": [], \n+ "label": null, \n+ "name": "Sort", \n+ "outputs": [\n+ {\n+ "name": "out_file1", \n+ "type": "input"\n+ }\n+ ], \n+ "position": {\n+ "left": 1056, \n+ "top": 506\n+ }, \n+ "post_job_actions": {\n+ "RenameDatasetActionout_file1": {\n+ "action_arguments": {\n+ "newname": "Top BLAST hit species counts"\n+ }, \n+ "action_type": "RenameDatasetAction", \n+ "output_name": "out_file1"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "sort1", \n+ "tool_state": "{\\"__page__\\": 0, \\"style\\": \\"\\\\\\"num\\\\\\"\\", \\"column\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": \\\\\\"1\\\\\\"}\\", \\"__rerun_remap_job_id__\\": null, \\"column_set\\": \\"[]\\", \\"input\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/mnt/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"order\\": \\"\\\\\\"DESC\\\\\\"\\"}", \n+ "tool_version": "1.0.3", \n+ "type": "tool", \n+ "user_outputs": [], \n+ "uuid": "c81cc61d-52a3-44ee-b646-b23e0e004c38"\n+ }\n+ }, \n+ "uuid": "9fe8754a-3a87-4f6a-89a2-141b02b4793e"\n+}\n\\ No newline at end of file\n'

diff -r 3b5eecc9551e -r 2c8931827fa5 blast_top_hit_species.png

Binary file blast_top_hit_species.png has changed

diff -r 3b5eecc9551e -r 2c8931827fa5 repository_dependencies.xml
--- a/repository_dependencies.xml Fri Oct 25 10:22:35 2013 -0400
+++ b/repository_dependencies.xml Mon Mar 30 11:46:13 2015 -0400

@@ -1,7 +1,9 @@
<?xml version="1.0"?>
-<repositories description="This requires my SignalP and TMHMM wrapers, and my FASTA filtering tool.">
-    
-    <repository changeset_revision="ee10017fcd80" name="tmhmm_and_signalp" owner="peterjc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    
-    <repository changeset_revision="8a34c565a473" name="seq_filter_by_id" owner="peterjc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+<repositories description="This workflow requires the NCBI BLAST+ tools etc">
+    <repository changeset_revision="5e9d5e536b79" name="ncbi_blast_plus" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="ae709fd50581" name="fasta_to_tabular" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="4231c585b6dd" name="sample_seqs" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="2064ae2602b1" name="unique" owner="bgruening" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    
</repositories>

diff -r 3b5eecc9551e -r 2c8931827fa5 secreted_protein_workflow.ga
--- a/secreted_protein_workflow.ga Fri Oct 25 10:22:35 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,288 +0,0 @@\n-{\n- "a_galaxy_workflow": "true", \n- "annotation": "Runs SignalP v3.0 and TMHMM v2.0 to look for secreted proteins.<br />\\n<br />\\nThis workflow is <a href=\\"http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow\\" target=\\"_blank\\">available on the Galaxy Tool Shed</a> with a README file giving more information including sample data, and full citation details (Cock and Pritchard 2014).", \n- "format-version": "0.1", \n- "name": "Find secreted proteins with TMHMM and SignalP", \n- "steps": {\n- "0": {\n- "annotation": "", \n- "id": 0, \n- "input_connections": {}, \n- "inputs": [\n- {\n- "description": "", \n- "name": "Input Dataset"\n- }\n- ], \n- "name": "Input dataset", \n- "outputs": [], \n- "position": {\n- "left": 200, \n- "top": 200\n- }, \n- "tool_errors": null, \n- "tool_id": null, \n- "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n- "tool_version": null, \n- "type": "data_input", \n- "user_outputs": []\n- }, \n- "1": {\n- "annotation": "", \n- "id": 1, \n- "input_connections": {\n- "fasta_file": {\n- "id": 0, \n- "output_name": "output"\n- }\n- }, \n- "inputs": [\n- {\n- "description": "runtime parameter for tool SignalP 3.0", \n- "name": "organism"\n- }\n- ], \n- "name": "SignalP 3.0", \n- "outputs": [\n- {\n- "name": "tabular_file", \n- "type": "tabular"\n- }\n- ], \n- "position": {\n- "left": 240, \n- "top": 341\n- }, \n- "post_job_actions": {\n- "HideDatasetActiontabular_file": {\n- "action_arguments": {}, \n- "action_type": "HideDatasetAction", \n- "output_name": "tabular_file"\n- }\n- }, \n- "tool_errors": null, \n- "tool_id": "signalp3", \n- "tool_state": "{\\"__page__\\": 0, \\"truncate\\": \\"\\\\\\"60\\\\\\"\\", \\"chromInfo\\": \\"\\\\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"fasta_file\\": \\"null\\", \\"organism\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"__rerun_remap_job_id__\\": null}", \n- "tool_version": "0.0.12", \n- "type": "tool", \n- "user_outputs": []\n- }, \n- "2": {\n- "annotation": "Select proteins with predicted signal peptide (SignalP NN D-Score or HMM)", \n- "id": 2, \n- "input_connections": {\n- "input": {\n- "id": 1, \n- "output_name": "tabular_file"\n- }\n- }, \n- "inputs": [], \n- "name": "Filter", \n- "outputs": [\n- {\n- "name": "out_file1", \n- "type": "input"\n- }\n- ], \n- "position": {\n- "left": 323, \n- "top": 528\n- }, \n- "post_job_actions": {\n- "HideDatasetActionout_file1": {\n- "action_arguments": {}, \n- "action_type": "HideDatasetAction", \n- "output_name": "out_file1"\n- }, \n- "RenameDatasetActionout_file1": {\n- "action_arguments": {\n- "newname": "Filtered SignalP results"\n- }, \n- "action_type": "RenameDatasetAction", \n- "output_name": "out_file1"\n- }\n- }, \n- "tool_errors": null,'..b'-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"__rerun_remap_job_id__\\": null}", \n- "tool_version": "0.0.11", \n- "type": "tool", \n- "user_outputs": []\n- }, \n- "5": {\n- "annotation": "Select proteins with no predicted transmembrane helices.", \n- "id": 5, \n- "input_connections": {\n- "input": {\n- "id": 4, \n- "output_name": "tabular_file"\n- }\n- }, \n- "inputs": [], \n- "name": "Filter", \n- "outputs": [\n- {\n- "name": "out_file1", \n- "type": "input"\n- }\n- ], \n- "position": {\n- "left": 729, \n- "top": 566\n- }, \n- "post_job_actions": {\n- "HideDatasetActionout_file1": {\n- "action_arguments": {}, \n- "action_type": "HideDatasetAction", \n- "output_name": "out_file1"\n- }, \n- "RenameDatasetActionout_file1": {\n- "action_arguments": {\n- "newname": "Filtered TMHMM results"\n- }, \n- "action_type": "RenameDatasetAction", \n- "output_name": "out_file1"\n- }\n- }, \n- "tool_errors": null, \n- "tool_id": "Filter1", \n- "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"cond\\": \\"\\\\\\"c5== 0\\\\\\"\\", \\"input\\": \\"null\\", \\"header_lines\\": \\"\\\\\\"0\\\\\\"\\", \\"chromInfo\\": \\"\\\\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\"}", \n- "tool_version": "1.1.0", \n- "type": "tool", \n- "user_outputs": []\n- }, \n- "6": {\n- "annotation": "Select those sequences with no transmembrane helices (from those with signal peptides).", \n- "id": 6, \n- "input_connections": {\n- "input_file": {\n- "id": 3, \n- "output_name": "output_pos"\n- }, \n- "input_tabular": {\n- "id": 5, \n- "output_name": "out_file1"\n- }\n- }, \n- "inputs": [], \n- "name": "Filter sequences by ID", \n- "outputs": [\n- {\n- "name": "output_pos", \n- "type": "fasta"\n- }, \n- {\n- "name": "output_neg", \n- "type": "fasta"\n- }\n- ], \n- "position": {\n- "left": 893, \n- "top": 281\n- }, \n- "post_job_actions": {\n- "HideDatasetActionoutput_neg": {\n- "action_arguments": {}, \n- "action_type": "HideDatasetAction", \n- "output_name": "output_neg"\n- }, \n- "RenameDatasetActionoutput_pos": {\n- "action_arguments": {\n- "newname": "Secreted proteins"\n- }, \n- "action_type": "RenameDatasetAction", \n- "output_name": "output_pos"\n- }\n- }, \n- "tool_errors": null, \n- "tool_id": "seq_filter_by_id", \n- "tool_state": "{\\"__page__\\": 0, \\"output_choice_cond\\": \\"{\\\\\\"output_choice\\\\\\": \\\\\\"pos\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"input_file\\": \\"null\\", \\"__rerun_remap_job_id__\\": null, \\"input_tabular\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"columns\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": [\\\\\\"1\\\\\\"]}\\"}", \n- "tool_version": "0.0.5", \n- "type": "tool", \n- "user_outputs": []\n- }\n- }\n-}\n\\ No newline at end of file\n'