Add --ensure_metadata --urls to planemo shed_lint. Fix many .shed.yml…

… files

.travis.yml

@@ -15,7 +15,7 @@ before_install:
   - export PLANEMO_CONDA_PREFIX="$HOME/conda"
 
 install:
-  - pip install -q flake8 planemo
+  - pip install flake8 planemo
   - planemo conda_init
   - export PATH="$PLANEMO_CONDA_PREFIX/bin:$PATH"
   - conda create -y -q -c bioconda --name iuc_conda samtools=0.1.19 bcftools
@@ -32,11 +32,11 @@ install:
   - cat changed_repositories_chunk.list
 
 script:
-  - cd "$TRAVIS_BUILD_DIR" && flake8 -v --exclude=.git .
+  - cd "$TRAVIS_BUILD_DIR" && flake8 --exclude=.git .
   - |
       cat changed_repositories_chunk.list
       export PLANEMO_TEST_RUN=True
-      while read -r DIR; do planemo shed_lint --report_level warn --tools --fail_level error --recursive "$DIR"; done < changed_repositories_chunk.list
+      while read -r DIR; do planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error --recursive "$DIR"; done < changed_repositories_chunk.list
       while read -r DIR; do planemo conda_install "$DIR"; done < changed_repositories_chunk.list
       while read -r DIR; do planemo test --conda_dependency_resolution --galaxy_branch $GALAXY_RELEASE --galaxy_source $GALAXY_REPO "$DIR" || exit 1; done < changed_repositories_chunk.list
 

data_managers/data_manager_bowtie_index_builder/.shed.yml

@@ -1,6 +1,7 @@
 categories:
 - Data Managers
 description: Data Manager for building bowtie indexes
+homepage_url: http://bowtie-bio.sourceforge.net/
 long_description: |
   Bowtie is an ultrafast, memory-efficient short read aligner. It
   aligns short DNA sequences (reads) to the human genome at a rate of over 25 million

data_managers/data_manager_hisat2_index_builder/.shed.yml

@@ -1,6 +1,7 @@
 categories:
 - Data Managers
 description: HISAT is a fast and sensitive spliced alignment program.
+homepage_url: http://ccb.jhu.edu/software/hisat2/
 long_description: |
   As part of HISAT, we have developed a new indexing scheme based on
   the Burrows-Wheeler transform (BWT) and the FM index, called
@@ -27,8 +28,6 @@ long_description: |
   with a large number of other tools (e.g. SAMtools, GATK) that use
   SAM. HISAT is distributed under the GPLv3 license, and it runs on
   the command line under Linux, Mac OS X and Windows.
-  
-  http://ccb.jhu.edu/software/hisat/index.shtml
 name: data_manager_hisat2_index_builder
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder

data_managers/data_manager_snpeff/.shed.yml

@@ -1,11 +1,10 @@
 categories:
 - Data Managers
 description: Manage SnpEff genome reference data
+homepage_url: http://snpeff.sourceforge.net/
 long_description: |
-  Data managers for the Galaxy admin to download SnpEff genome databases. 
-  SnpEff is developed by Pablo Cingolani at http://snpeff.sourceforge.net/
-
+  Data managers for the Galaxy admin to download SnpEff genome databases
 name: data_manager_snpeff
 owner: iuc
-remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff
 type: unrestricted

data_managers/data_manager_snpsift_dbnsfp/.shed.yml

@@ -1,15 +1,12 @@
 categories:
 - Data Managers
-description: Install SnpSift dbNSFP local data 
+description: Install SnpSift dbNSFP local data
+homepage_url: http://snpeff.sourceforge.net/SnpSift.html#dbNSFP
 long_description: |
   Installs dbNSFP data for use by SnpSift dbNSFP
   dbNSFP is an integrated database of human functional predictions 
   from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.)
-
-  SnpEff and SnpSift are developed by Pablo Cingolani.
-  http://snpeff.sourceforge.net/SnpSift.html#dbNSFP
-
 name: data_manager_snpsift_dbnsfp
 owner: iuc
-remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp
 type: unrestricted

packages/package_aragorn_1_2_36/.shed.yml

@@ -2,10 +2,9 @@ categories:
 - Tool Dependency Packages
 description: Contains a tool dependency definition that downloads and extract version
   1.2.36 of Aragorn.
+homepage_url: http://mbio-serv2.mbioekol.lu.se/ARAGORN/
 long_description: |
   ARAGORN, tRNA (and tmRNA) detection.
-
-  http://www.ncbi.nlm.nih.gov/pubmed/14704338
 name: package_aragorn_1_2_36
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_aragorn_1_2_36

packages/package_art_2014_11_03/.shed.yml

@@ -2,6 +2,7 @@ categories:
 - Tool Dependency Packages
 description: Contains a tool dependency definition that downloads and extract version
   2014.11.03 (vanilla ice cream) of ART.
+homepage_url: http://www.niehs.nih.gov/research/resources/software/biostatistics/art/
 long_description: |
   ART is a set of simulation tools to generate synthetic next-generation
   sequencing reads. ART simulates sequencing reads by mimicking real sequencing
@@ -18,8 +19,6 @@ long_description: |
   simulation. ART outputs reads in the FASTQ format, and alignments in the ALN
   format. ART can also generate alignments in the SAM alignment or UCSC BED
   file format.
-
-  http://www.niehs.nih.gov/research/resources/software/biostatistics/art/
 name: package_art_2014_11_03
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03

packages/package_atlas_3_10/.shed.yml

@@ -1,13 +1,12 @@
 categories:
 - Tool Dependency Packages
 description: Automatically Tuned Linear Algebra Software
+homepage_url: http://math-atlas.sourceforge.net/
 long_description: |
   The ATLAS (Automatically Tuned Linear Algebra Software) project
   is an ongoing research effort focusing on applying empirical techniques in order
   to provide portable performance. At present, it provides C and Fortran77 interfaces
   to a portably efficient BLAS implementation, as well as a few routines from LAPACK.
-
-  http://math-atlas.sourceforge.net/
 name: package_atlas_3_10
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10

packages/package_atlas_3_11/.shed.yml

@@ -1,13 +1,12 @@
 categories:
 - Tool Dependency Packages
 description: Automatically Tuned Linear Algebra Software
+homepage_url: http://math-atlas.sourceforge.net/
 long_description: |
   The ATLAS (Automatically Tuned Linear Algebra Software) project
   is an ongoing research effort focusing on applying empirical techniques in order
   to provide portable performance. At present, it provides C and Fortran77 interfaces
   to a portably efficient BLAS implementation, as well as a few routines from LAPACK.
-
-  http://math-atlas.sourceforge.net/
 name: package_atlas_3_11
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11

packages/package_ballgown_1_0_3/.shed.yml

@@ -2,10 +2,9 @@ categories:
 - Tool Dependency Packages
 description: Contains a tool dependency definition that downloads and installs version
   1.0.3 of the ballgown.
+homepage_url: https://github.com/alyssafrazee/ballgown
 long_description: |
-  Ballgown is a software package designed to facilitate flexible differential expression analysis of RNA-seq data. 
-
-  https://github.com/alyssafrazee/ballgown
+  Ballgown is a software package designed to facilitate flexible differential expression analysis of RNA-seq data.
 name: package_ballgown_1_0_3
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_ballgown_1_0_3

packages/package_bcftools_1_3/.shed.yml

@@ -2,7 +2,7 @@ categories:
  - Tool Dependency Packages
  - Variant Analysis
 description: Contains a tool dependency definition that downloads and extracts version 1.3 of bcftools
-homepage_url: https://github.com/galaxyproject/tools-iuc/
+homepage_url: https://samtools.github.io/bcftools/
 long_description: 'BCFtools is a set of utilities that manipulate variant calls in
   the Variant Call Format (VCF) and its binary counterpart BCF. All commands work
   transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
@@ -13,4 +13,5 @@ long_description: 'BCFtools is a set of utilities that manipulate variant calls
   Un-indexed VCF and BCF and streams will work in most, but not all situations.'
 name: package_bcftools_1_3
 owner: iuc
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_bcftools_1_3/
 type: tool_dependency_definition

packages/package_chemfp_1_1/.shed.yml

@@ -2,12 +2,11 @@ categories:
 - Tool Dependency Packages
 description: Contains a tool dependency definition that downloads and compiles version
   1.1.x of the chemfp package.
+homepage_url: http://chemfp.com/
 long_description: |
   Chemfp provides toolkit independent generation of fingerprints
   and high-performance similarity search. The tools support the FPS fingerprint
   file format.
-
-  http://chemfp.com/
 name: package_chemfp_1_1
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_chemfp_1_1

packages/package_picard_2_0_1/.shed.yml

@@ -3,6 +3,9 @@ categories:
 description: Contains a tool dependency definition that downloads and compiles version
   2.0.1 of the Picard package.
 homepage_url: http://broadinstitute.github.io/picard/
+long_description: |
+  Picard is a set of command line tools for manipulating high-throughput
+  sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
 name: package_picard_2_0_1
 owner: devteam
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_picard_2_0_1

packages/package_r_crisprseek_1_11_0/.shed.yml

@@ -8,7 +8,5 @@ description: Contains a tool dependency definition that downloads version
 long_description: |
   CRISPRseek is a Bioconductor package for design of targer-specific guide RNAs
   in CRISPR-Cas9, genome-editing systems
-
-  http://www.bioconductor.org/packages/release/bioc/html/CRISPRseek.html
 homepage_url:  http://www.bioconductor.org/packages/release/bioc/html/CRISPRseek.html
-remote_repository_url: https://github.com/galaxyproject/tools-iuc/packages/package_r_crisprseek_1_11_0
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_crisprseek_1_11_0

suites/suite_fasta_tools/.shed.yml

@@ -1,6 +1,7 @@
 categories:
 - Sequence Analysis
 description: Contains tools for manipulating FASTA files
+homepage_url: https://github.com/galaxyproject/tools-iuc/
 long_description: |
   Various tools to manipulate and filter FASTA file, maintained by the Galaxy community.
 name: suite_fasta_tools

tools/weather_app/.shed.yml

@@ -2,9 +2,10 @@
 owner: iuc
 name: simpleweather
 description: provides simple weather in text format
+homepage_url: http://wttr.in/
 long_description: |
     Weather tool using
-    https://wttr.in
+    http://wttr.in
     The tool should be treated carefully because it uses an external webpage.
 categories:
     - Visualization

tools/xpath/.shed.yml

@@ -1,6 +1,7 @@
 categories:
 - Text Manipulation
 description: XPath XML querying tool
+homepage_url: http://search.cpan.org/dist/XML-XPath/
 long_description: |
   Execute XPath queries on XML files for use in downstream analysis. Useful for
   extracting lists of IDs or blast hits from large XML files.